Merge cgal_4.8_issue branch into the trunk

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2242 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 094b70b4141e7456651263b1619240aff6a5d562

22 files changed, 523 insertions, 619 deletions

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 36e8afd7..18cd0ca2 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -5,176 +5,88 @@ include(CMakeGUDHIVersion.txt)
 # Generate GUDHI official version file
 configure_file(GUDHIVersion.cmake.in "${CMAKE_SOURCE_DIR}/GUDHIVersion.cmake" @ONLY)
 
-find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework chrono timer date_time program_options thread REQUIRED)
-
-if(NOT Boost_FOUND)
-  message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.")
+set(CMAKE_PREFIX_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/")
+set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/")
+message("CMAKE_PREFIX_PATH = ${CMAKE_PREFIX_PATH}")
+message("CMAKE_MODULE_PATH = ${CMAKE_MODULE_PATH}")
+
+enable_testing()
+
+# For "make user_version"
+include("${CMAKE_MODULE_PATH}/GUDHI_user_version_target.txt")
+# For "make doxygen"
+include("${CMAKE_MODULE_PATH}/GUDHI_doxygen_target.txt")
+# For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH
+include("${CMAKE_MODULE_PATH}/GUDHI_third_party_libraries.txt")
+
+if(MSVC)
+  # Turn off some VC++ warnings
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018")
 else()
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic")
+endif()
 
-  set(CMAKE_PREFIX_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/")
-  set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/src/cmake/modules/")
-  message("CMAKE_PREFIX_PATH = ${CMAKE_PREFIX_PATH}")
-  message("CMAKE_MODULE_PATH = ${CMAKE_MODULE_PATH}")
-
-  enable_testing()
-
-  # For "make user_version"
-  include(${CMAKE_MODULE_PATH}/GUDHI_user_version_target.txt)
-  # For "make doxygen"
-  include(${CMAKE_MODULE_PATH}/GUDHI_doxygen_target.txt)
-
-  find_package(GMP)
-  if(GMP_FOUND)
-    message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}")
-    INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
-    find_package(GMPXX)
-    if(GMPXX_FOUND)
-      message(STATUS "GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
-      INCLUDE_DIRECTORIES(${GMPXX_INCLUDE_DIR})
-    endif()
-  endif()
-
-  # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CMAKE_CXX_FLAGS are overwritten.
-  # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
-  # A workaround is to include(${CGAL_USE_FILE}) before adding "-std=c++11".
-  # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
-  # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
-  # but it implies to use cmake version 3.1 at least.
-  find_package(CGAL)
-  # Only CGAL versions > 4.4 supports what Gudhi uses from CGAL
-  if (CGAL_VERSION VERSION_LESS 4.4.0)
-    message("CGAL version ${CGAL_VERSION} is considered too old to be used by Gudhi.")
-    unset(CGAL_FOUND)
-  endif()
-  if(CGAL_FOUND)
-    message(STATUS "CGAL version: ${CGAL_VERSION}.")
-    include( ${CGAL_USE_FILE} )
-
-    if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-      include_directories(BEFORE "src/common/include/gudhi_patches")
-    endif()
-  endif()
-  
-  if(MSVC)
-    # Turn off some VC++ warnings
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018")
-  else()
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic")
-  endif()
-
-  if(CMAKE_BUILD_TYPE MATCHES Debug)
-    message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}")
-  else()
-    message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
-  endif()
-
-  set(Boost_USE_STATIC_LIBS        ON)
-  set(Boost_USE_MULTITHREADED      ON)
-  set(Boost_USE_STATIC_RUNTIME    OFF)
-
-  # Find TBB package for parallel sort - not mandatory, just optional.
-  set(TBB_FIND_QUIETLY ON)
-  find_package(TBB)
-  if (TBB_FOUND)
-    include(${TBB_USE_FILE})
-    message("TBB found in ${TBB_LIBRARY_DIRS}")
-    add_definitions(-DGUDHI_USE_TBB)
-  endif()
-
-  find_package(Eigen3 3.1.0)
-  if (EIGEN3_FOUND)
-    message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
-    include( ${EIGEN3_USE_FILE} )
-    #include_directories (BEFORE "../../include")
-  endif (EIGEN3_FOUND)
-
-  # Required programs for unitary tests purpose
-  FIND_PROGRAM( GCOVR_PATH gcovr )
-  if (GCOVR_PATH)
-    message("gcovr found in ${GCOVR_PATH}")
-  endif()
-  # Required programs for unitary tests purpose
-  FIND_PROGRAM( GPROF_PATH gprof )
-  if (GPROF_PATH)
-    message("gprof found in ${GPROF_PATH}")
-  endif()
-  FIND_PROGRAM( DIFF_PATH diff )
-  if (DIFF_PATH)
-    message("diff found in ${DIFF_PATH}")
-  endif()
-
-  # BOOST ISSUE result_of vs C++11
-  add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE)
-  # BOOST ISSUE with Libraries name resolution under Windows
-  add_definitions(-DBOOST_ALL_NO_LIB)
-  # problem with Visual Studio link on Boost program_options
-  add_definitions( -DBOOST_ALL_DYN_LINK )
-
-  INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
-  LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})                      
-
-  message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
-  message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
-
-  if (DEBUG_TRACES)
-    # For programs to be more verbose
-    message(STATUS "DEBUG_TRACES are activated")
-    add_definitions(-DDEBUG_TRACES)
-  endif()
-
-  include_directories(src/common/include/)
-  include_directories(src/Alpha_complex/include/)
-  include_directories(src/Bitmap_cubical_complex/include/)
-  include_directories(src/Bottleneck_distance/include/)
-  include_directories(src/Contraction/include/)
-  include_directories(src/Hasse_complex/include/)
-  include_directories(src/Persistent_cohomology/include/)
-  include_directories(src/Rips_complex/include/)
-  include_directories(src/Simplex_tree/include/)
-  include_directories(src/Skeleton_blocker/include/)
-  include_directories(src/Spatial_searching/include/)
-  include_directories(src/Subsampling/include/)
-  include_directories(src/Tangential_complex/include/)
-  include_directories(src/Witness_complex/include/)
-
-  add_subdirectory(src/common/example)
-  add_subdirectory(src/common/test)
-  add_subdirectory(src/Simplex_tree/test)
-  add_subdirectory(src/Simplex_tree/example)
-  add_subdirectory(src/Persistent_cohomology/test)
-  add_subdirectory(src/Persistent_cohomology/example)
-  add_subdirectory(src/Persistent_cohomology/benchmark)
-  add_subdirectory(src/Skeleton_blocker/test) 
-  add_subdirectory(src/Skeleton_blocker/example) 
-  add_subdirectory(src/Contraction/example)
-  add_subdirectory(src/Witness_complex/test)
-  add_subdirectory(src/Witness_complex/example)
-  add_subdirectory(src/Bitmap_cubical_complex/test)
-  add_subdirectory(src/Bitmap_cubical_complex/example)
-  add_subdirectory(src/Alpha_complex/example)
-  add_subdirectory(src/Alpha_complex/test)
-  add_subdirectory(src/Spatial_searching/example)
-  add_subdirectory(src/Spatial_searching/test)
-  add_subdirectory(src/Subsampling/example)
-  add_subdirectory(src/Subsampling/test)
-  add_subdirectory(src/Tangential_complex/example)
-  add_subdirectory(src/Tangential_complex/test)
-  add_subdirectory(src/Tangential_complex/benchmark)
-  add_subdirectory(src/Bottleneck_distance/example)
-  add_subdirectory(src/Bottleneck_distance/test)
-  add_subdirectory(src/Bottleneck_distance/benchmark)
-  add_subdirectory(src/Rips_complex/example)
-  add_subdirectory(src/Rips_complex/test)
-
-  # data points generator
-  add_subdirectory(data/points/generator)
-
-  add_subdirectory(src/GudhUI)
-
-  # This variable is used by Cython CMakeLists.txt to know its path
-  set(GUDHI_CYTHON_PATH "src/cython")
-  add_subdirectory(${GUDHI_CYTHON_PATH})
-
-endif()  
-
-
+if(CMAKE_BUILD_TYPE MATCHES Debug)
+  message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}")
+else()
+  message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
+endif()
+
+if (DEBUG_TRACES)
+  # For programs to be more verbose
+  message(STATUS "DEBUG_TRACES are activated")
+  add_definitions(-DDEBUG_TRACES)
+endif()
+
+include_directories(src/common/include/)
+include_directories(src/Alpha_complex/include/)
+include_directories(src/Bitmap_cubical_complex/include/)
+include_directories(src/Bottleneck_distance/include/)
+include_directories(src/Contraction/include/)
+include_directories(src/Hasse_complex/include/)
+include_directories(src/Persistent_cohomology/include/)
+include_directories(src/Rips_complex/include/)
+include_directories(src/Simplex_tree/include/)
+include_directories(src/Skeleton_blocker/include/)
+include_directories(src/Spatial_searching/include/)
+include_directories(src/Subsampling/include/)
+include_directories(src/Tangential_complex/include/)
+include_directories(src/Witness_complex/include/)
+
+add_subdirectory(src/common/example)
+add_subdirectory(src/common/test)
+add_subdirectory(src/Simplex_tree/test)
+add_subdirectory(src/Simplex_tree/example)
+add_subdirectory(src/Persistent_cohomology/test)
+add_subdirectory(src/Persistent_cohomology/example)
+add_subdirectory(src/Persistent_cohomology/benchmark)
+add_subdirectory(src/Skeleton_blocker/test)
+add_subdirectory(src/Skeleton_blocker/example)
+add_subdirectory(src/Contraction/example)
+add_subdirectory(src/Witness_complex/test)
+add_subdirectory(src/Witness_complex/example)
+add_subdirectory(src/Bitmap_cubical_complex/test)
+add_subdirectory(src/Bitmap_cubical_complex/example)
+add_subdirectory(src/Alpha_complex/example)
+add_subdirectory(src/Alpha_complex/test)
+add_subdirectory(src/Spatial_searching/example)
+add_subdirectory(src/Spatial_searching/test)
+add_subdirectory(src/Subsampling/example)
+add_subdirectory(src/Subsampling/test)
+add_subdirectory(src/Tangential_complex/example)
+add_subdirectory(src/Tangential_complex/test)
+add_subdirectory(src/Tangential_complex/benchmark)
+add_subdirectory(src/Bottleneck_distance/example)
+add_subdirectory(src/Bottleneck_distance/test)
+add_subdirectory(src/Bottleneck_distance/benchmark)
+add_subdirectory(src/Rips_complex/example)
+add_subdirectory(src/Rips_complex/test)
+
+# data points generator
+add_subdirectory(data/points/generator)
+
+add_subdirectory(src/GudhUI)
+
+# This variable is used by Cython CMakeLists.txt to know its path
+set(GUDHI_CYTHON_PATH "src/cython")
+add_subdirectory(${GUDHI_CYTHON_PATH})
diff --git a/data/points/generator/CMakeLists.txt b/data/points/generator/CMakeLists.txt
index f559610c..9a7f7bce 100644
--- a/data/points/generator/CMakeLists.txt
+++ b/data/points/generator/CMakeLists.txt
@@ -1,18 +1,14 @@
 cmake_minimum_required(VERSION 2.6)
 project(Data_points_generator)
 
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    if (EIGEN3_FOUND)
-      add_executable ( hypergenerator hypergenerator.cpp )
-      target_link_libraries(hypergenerator ${Boost_SYSTEM_LIBRARY})
-      add_test(hypergenerator_on_sphere_3000_10_5.0 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator on sphere onSphere.off 3000 10 5.0)
-      add_test(hypergenerator_on_sphere_10000_3 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator on sphere onSphere.off 10000 3)
-      add_test(hypergenerator_in_sphere_7000_12_10.8 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in sphere inSphere.off 7000 12 10.8)
-      add_test(hypergenerator_in_sphere_50000_2 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in sphere inSphere.off 50000 2)
-      # on cube is not available in CGAL
-      add_test(hypergenerator_in_cube_7000_12_10.8 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in cube inCube.off 7000 12 10.8)
-      add_test(hypergenerator_in_cube_50000_2 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in cube inCube.off 50000 3)
-      endif(EIGEN3_FOUND)
-  endif(NOT CGAL_VERSION VERSION_LESS 4.6.0)
-endif(CGAL_FOUND)
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+  add_executable ( hypergenerator hypergenerator.cpp )
+  target_link_libraries(hypergenerator ${Boost_SYSTEM_LIBRARY})
+  add_test(hypergenerator_on_sphere_3000_10_5.0 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator on sphere onSphere.off 3000 10 5.0)
+  add_test(hypergenerator_on_sphere_10000_3 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator on sphere onSphere.off 10000 3)
+  add_test(hypergenerator_in_sphere_7000_12_10.8 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in sphere inSphere.off 7000 12 10.8)
+  add_test(hypergenerator_in_sphere_50000_2 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in sphere inSphere.off 50000 2)
+  # on cube is not available in CGAL
+  add_test(hypergenerator_in_cube_7000_12_10.8 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in cube inCube.off 7000 12 10.8)
+  add_test(hypergenerator_in_cube_50000_2 ${CMAKE_CURRENT_BINARY_DIR}/hypergenerator in cube inCube.off 50000 3)
+endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt
index 71a95d61..b9bcdb55 100644
--- a/src/Alpha_complex/example/CMakeLists.txt
+++ b/src/Alpha_complex/example/CMakeLists.txt
@@ -2,32 +2,28 @@ cmake_minimum_required(VERSION 2.6)
 project(Alpha_complex_examples)
 
 # need CGAL 4.7
-# cmake -DCGAL_DIR=~/workspace/CGAL-4.7-Ic-41 ../../..
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-    if (EIGEN3_FOUND)
-      add_executable ( alphapoints Alpha_complex_from_points.cpp )
-      target_link_libraries(alphapoints  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY})
-      add_executable ( alphaoffreader Alpha_complex_from_off.cpp )
-      target_link_libraries(alphaoffreader  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY})
-      if (TBB_FOUND)
-        target_link_libraries(alphapoints ${TBB_LIBRARIES})
-        target_link_libraries(alphaoffreader ${TBB_LIBRARIES})
-      endif()
+# cmake -DCGAL_DIR=~/workspace/CGAL-4.7 ..
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+  add_executable ( alphapoints Alpha_complex_from_points.cpp )
+  target_link_libraries(alphapoints  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY})
+  add_executable ( alphaoffreader Alpha_complex_from_off.cpp )
+  target_link_libraries(alphaoffreader  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(alphapoints ${TBB_LIBRARIES})
+    target_link_libraries(alphaoffreader ${TBB_LIBRARIES})
+  endif()
 
-      add_test(alphapoints ${CMAKE_CURRENT_BINARY_DIR}/alphapoints)
-      # Do not forget to copy test files in current binary dir
-      file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-      add_test(alphaoffreader_doc_60 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 60.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt)
-      add_test(alphaoffreader_doc_32 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 32.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt)
-      if (DIFF_PATH)
-        # Do not forget to copy test results files in current binary dir
-        file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-        file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+  add_test(alphapoints ${CMAKE_CURRENT_BINARY_DIR}/alphapoints)
+  # Do not forget to copy test files in current binary dir
+  file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+  add_test(alphaoffreader_doc_60 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 60.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt)
+  add_test(alphaoffreader_doc_32 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 32.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt)
+  if (DIFF_PATH)
+    # Do not forget to copy test results files in current binary dir
+    file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+    file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-        add_test(alphaoffreader_doc_60_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt)
-        add_test(alphaoffreader_doc_32_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt)
-      endif()
-    endif(EIGEN3_FOUND)
-  endif(NOT CGAL_VERSION VERSION_LESS 4.7.0)
-endif(CGAL_FOUND)
+    add_test(alphaoffreader_doc_60_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt)
+    add_test(alphaoffreader_doc_32_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt)
+  endif()
+endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt
index efc0565f..32091196 100644
--- a/src/Alpha_complex/test/CMakeLists.txt
+++ b/src/Alpha_complex/test/CMakeLists.txt
@@ -10,23 +10,19 @@ if (GPROF_PATH)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
 endif()
 
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-    if (EIGEN3_FOUND)
-      add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp )
-      target_link_libraries(AlphaComplexUT  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
-      if (TBB_FOUND)
-        target_link_libraries(AlphaComplexUT ${TBB_LIBRARIES})
-      endif()
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+  add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp )
+  target_link_libraries(AlphaComplexUT  ${Boost_SYSTEM_LIBRARY} ${Boost_THREAD_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(AlphaComplexUT ${TBB_LIBRARIES})
+  endif()
 
-      # Do not forget to copy test files in current binary dir
-      file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+  # Do not forget to copy test files in current binary dir
+  file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
-      add_test(AlphaComplexUT ${CMAKE_CURRENT_BINARY_DIR}/AlphaComplexUT
-      # XML format for Jenkins xUnit plugin 
-      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/AlphaComplexUT.xml --log_level=test_suite --report_level=no)
+  add_test(AlphaComplexUT ${CMAKE_CURRENT_BINARY_DIR}/AlphaComplexUT
+  # XML format for Jenkins xUnit plugin
+  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/AlphaComplexUT.xml --log_level=test_suite --report_level=no)
 
-    endif(EIGEN3_FOUND)
-  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-endif(CGAL_FOUND)
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
 
diff --git a/src/Bottleneck_distance/benchmark/CMakeLists.txt b/src/Bottleneck_distance/benchmark/CMakeLists.txt
index c99e0373..170081ce 100644
--- a/src/Bottleneck_distance/benchmark/CMakeLists.txt
+++ b/src/Bottleneck_distance/benchmark/CMakeLists.txt
@@ -1,14 +1,9 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_benchmark)
 
-
-# requires CGAL 4.8
-# cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../..
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    add_executable ( bottleneck_chrono bottleneck_chrono.cpp )
-    if (TBB_FOUND)
-      target_link_libraries(bottleneck_chrono ${TBB_LIBRARIES})
-    endif(TBB_FOUND)
-  endif ()
-endif()
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable ( bottleneck_chrono bottleneck_chrono.cpp )
+  if (TBB_FOUND)
+    target_link_libraries(bottleneck_chrono ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
+endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index 55f22c01..b0a19f8b 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -1,24 +1,20 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_examples)
 
-# requires CGAL 4.8
-# cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../..
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp)
-    add_executable (bottleneck_basic_example bottleneck_basic_example.cpp)
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp)
+  add_executable (bottleneck_basic_example bottleneck_basic_example.cpp)
 
-    add_test(bottleneck_basic_example ${CMAKE_CURRENT_BINARY_DIR}/bottleneck_basic_example)
+  add_test(bottleneck_basic_example ${CMAKE_CURRENT_BINARY_DIR}/bottleneck_basic_example)
 
-    add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
-    target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-    if (TBB_FOUND)
-      target_link_libraries(bottleneck_read_file_example ${TBB_LIBRARIES})
-      target_link_libraries(bottleneck_basic_example ${TBB_LIBRARIES})
-      target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
-    endif(TBB_FOUND)
-    add_test(alpha_rips_persistence_bottleneck_distance ${CMAKE_CURRENT_BINARY_DIR}/alpha_rips_persistence_bottleneck_distance
-        ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.15 -m 0.12 -d 3 -p 3)
+  add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
+  target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(bottleneck_read_file_example ${TBB_LIBRARIES})
+    target_link_libraries(bottleneck_basic_example ${TBB_LIBRARIES})
+    target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
+  add_test(alpha_rips_persistence_bottleneck_distance ${CMAKE_CURRENT_BINARY_DIR}/alpha_rips_persistence_bottleneck_distance
+      ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -r 0.15 -m 0.12 -d 3 -p 3)
 
-  endif ()
-endif()
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/test/CMakeLists.txt b/src/Bottleneck_distance/test/CMakeLists.txt
index 3e61f4cf..3d8e1f95 100644
--- a/src/Bottleneck_distance/test/CMakeLists.txt
+++ b/src/Bottleneck_distance/test/CMakeLists.txt
@@ -11,19 +11,15 @@ if (GPROF_PATH)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
 endif()
 
-# requires CGAL 4.8
-# cmake -DCGAL_DIR=~/workspace/CGAL-4.8 ../../..
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    add_executable ( bottleneckUT bottleneck_unit_test.cpp )
-    target_link_libraries(bottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
-    if (TBB_FOUND)
-      target_link_libraries(bottleneckUT ${TBB_LIBRARIES})
-    endif(TBB_FOUND)
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable ( bottleneckUT bottleneck_unit_test.cpp )
+  target_link_libraries(bottleneckUT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(bottleneckUT ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
 
-    # Unitary tests
-    add_test(NAME bottleneckUT COMMAND ${CMAKE_CURRENT_BINARY_DIR}/bottleneckUT
-      # XML format for Jenkins xUnit plugin
-      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/bottleneckUT.xml --log_level=test_suite --report_level=no)
-  endif ()
-endif()
+  # Unitary tests
+  add_test(NAME bottleneckUT COMMAND ${CMAKE_CURRENT_BINARY_DIR}/bottleneckUT
+    # XML format for Jenkins xUnit plugin
+    --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/bottleneckUT.xml --log_level=test_suite --report_level=no)
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index abd4d12c..4fa73662 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -9,154 +9,85 @@ enable_testing()
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/")
 
-find_package(Boost REQUIRED COMPONENTS system filesystem program_options chrono timer date_time REQUIRED)
+# For "make doxygen"
+set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR})
+include(${CMAKE_MODULE_PATH}/GUDHI_doxygen_target.txt)
 
-if(NOT Boost_FOUND)
-  message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.")
+# For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH
+include("${CMAKE_MODULE_PATH}/GUDHI_third_party_libraries.txt")
+
+if(MSVC)
+  # Turn off some VC++ warnings
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018")
 else()
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic")
+endif()
 
-  # For "make doxygen"
-  set(GUDHI_USER_VERSION_DIR ${CMAKE_SOURCE_DIR})
-  include(${CMAKE_MODULE_PATH}/GUDHI_doxygen_target.txt)
-
-  find_package(GMP)
-  if(GMP_FOUND)
-    message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}")
-    INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
-    find_package(GMPXX)
-    if(GMPXX_FOUND)
-      message(STATUS "GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
-      INCLUDE_DIRECTORIES(${GMPXX_INCLUDE_DIR})
-    endif()
-  endif()
-
-  # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CMAKE_CXX_FLAGS are overwritten.
-  # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
-  # A workaround is to include(${CGAL_USE_FILE}) before adding "-std=c++11".
-  # A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html 
-  # or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
-  # but it implies to use cmake version 3.1 at least.
-
-  # find CGAL in QUIET mode for cmake to be less verbose when CGAL is not found.
-  find_package(CGAL QUIET)
-  # Only CGAL versions > 4.4 supports what Gudhi uses from CGAL
-  if (CGAL_VERSION VERSION_LESS 4.4.0 AND CGAL_FOUND)
-    message("CGAL version ${CGAL_VERSION} is considered too old to be used by Gudhi.")
-    unset(CGAL_FOUND)
-  endif(CGAL_VERSION VERSION_LESS 4.4.0 AND CGAL_FOUND)
-  if(CGAL_FOUND)
-    message(STATUS "CGAL version: ${CGAL_VERSION}.")
-    include( ${CGAL_USE_FILE} )
-    
-    if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-      include_directories(BEFORE "include/gudhi_patches")
-    endif()
-  endif()
-  
-  if(MSVC)
-    # Turn off some VC++ warnings
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018")
-  else()
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic")
-  endif()
-
-  if(CMAKE_BUILD_TYPE MATCHES Debug)
-    message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}")
-  else()
-    message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
-  endif()
-
-  set(Boost_USE_STATIC_LIBS        ON)
-  set(Boost_USE_MULTITHREADED      ON)
-  set(Boost_USE_STATIC_RUNTIME    OFF)
-
-  # Find TBB package for parallel sort - not mandatory, just optional.
-  set(TBB_FIND_QUIETLY ON)
-  find_package(TBB)
-  if (TBB_FOUND)
-    include(${TBB_USE_FILE})
-    message("TBB found in ${TBB_LIBRARY_DIRS}")
-    add_definitions(-DGUDHI_USE_TBB)
-  endif()
-
-  find_package(Eigen3 3.1.0)
-  if (EIGEN3_FOUND)
-    message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
-    include( ${EIGEN3_USE_FILE} )
-    #include_directories (BEFORE "../../include")
-  endif (EIGEN3_FOUND)
-
-  # BOOST ISSUE result_of vs C++11
-  add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE)
-  # BOOST ISSUE with Libraries name resolution under Windows
-  add_definitions(-DBOOST_ALL_NO_LIB)
-  # problem with Visual Studio link on Boost program_options
-  add_definitions( -DBOOST_ALL_DYN_LINK )
-
-  INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
-  LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
-
-  if (DEBUG_TRACES)
-    message(STATUS "DEBUG_TRACES are activated")
-    # For programs to be more verbose
-    add_definitions(-DDEBUG_TRACES)
-  endif()
-
-  #---------------------------------------------------------------------------------------
-  # Gudhi compilation part
-  include_directories(include)
-
-  add_subdirectory(example/common)
-  add_subdirectory(example/Simplex_tree)                   
-  add_subdirectory(example/Persistent_cohomology)                   
-  add_subdirectory(example/Skeleton_blocker)                   
-  add_subdirectory(example/Contraction)                   
-  add_subdirectory(example/Bitmap_cubical_complex)
-  add_subdirectory(example/Witness_complex)
-  add_subdirectory(example/Alpha_complex)
-  add_subdirectory(example/Rips_complex)
-  add_subdirectory(example/Spatial_searching)
-  add_subdirectory(example/Subsampling)
-  add_subdirectory(example/Tangential_complex)
-  add_subdirectory(example/Bottleneck_distance)
-
-  # data points generator
-  add_subdirectory(data/points/generator)
-
-  # Please let GudhUI in last compilation position as QT is known to modify CMAKE_CXX_FLAGS
-  # GudhUI
-  add_subdirectory(GudhUI)
-
-  # This variable is used by Cython CMakeLists.txt to know its path
-  set(GUDHI_CYTHON_PATH "cython")
-  add_subdirectory(${GUDHI_CYTHON_PATH})
-  #---------------------------------------------------------------------------------------
-
-  #---------------------------------------------------------------------------------------
-  # GUDHIConfig.cmake
-  # Export the package for use from the build-tree
-  # (this registers the build-tree with a global CMake-registry)
-  export(PACKAGE GUDHI)
-
-  message("++ make install will install ${PROJECT_NAME} in the following directory : ${CMAKE_INSTALL_PREFIX}")
-  # Create the GUDHIConfig.cmake and GUDHIConfigVersion files
-  set(CONF_INCLUDE_DIRS "${CMAKE_INSTALL_PREFIX}/include")
-  configure_file(GUDHIConfig.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake" @ONLY)
-  configure_file(GUDHIConfigVersion.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake" @ONLY)
-
-  #---------------------------------------------------------------------------------------
-
-  #---------------------------------------------------------------------------------------
-  # Gudhi installation part
-
-  # Install the GUDHIConfig.cmake and GUDHIConfigVersion.cmake
-  install(FILES
-    "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake"
-    "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake"
-    DESTINATION share/gudhi)
-
-  # install the include file on "make install"
-  install(DIRECTORY include/gudhi DESTINATION include)
-  #---------------------------------------------------------------------------------------
-
-endif()  
+if(CMAKE_BUILD_TYPE MATCHES Debug)
+  message("++ Debug compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}")
+else()
+  message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
+endif()
+
+if (DEBUG_TRACES)
+  message(STATUS "DEBUG_TRACES are activated")
+  # For programs to be more verbose
+  add_definitions(-DDEBUG_TRACES)
+endif()
+
+#---------------------------------------------------------------------------------------
+# Gudhi compilation part
+include_directories(include)
+
+add_subdirectory(example/common)
+add_subdirectory(example/Simplex_tree)
+add_subdirectory(example/Persistent_cohomology)
+add_subdirectory(example/Skeleton_blocker)
+add_subdirectory(example/Contraction)
+add_subdirectory(example/Bitmap_cubical_complex)
+add_subdirectory(example/Witness_complex)
+add_subdirectory(example/Alpha_complex)
+add_subdirectory(example/Rips_complex)
+add_subdirectory(example/Spatial_searching)
+add_subdirectory(example/Subsampling)
+add_subdirectory(example/Tangential_complex)
+add_subdirectory(example/Bottleneck_distance)
+
+# data points generator
+add_subdirectory(data/points/generator)
+
+# Please let GudhUI in last compilation position as QT is known to modify CMAKE_CXX_FLAGS
+# GudhUI
+add_subdirectory(GudhUI)
+
+# This variable is used by Cython CMakeLists.txt to know its path
+set(GUDHI_CYTHON_PATH "cython")
+add_subdirectory(${GUDHI_CYTHON_PATH})
+#---------------------------------------------------------------------------------------
+
+#---------------------------------------------------------------------------------------
+# GUDHIConfig.cmake
+# Export the package for use from the build-tree
+# (this registers the build-tree with a global CMake-registry)
+export(PACKAGE GUDHI)
+
+message("++ make install will install ${PROJECT_NAME} in the following directory : ${CMAKE_INSTALL_PREFIX}")
+# Create the GUDHIConfig.cmake and GUDHIConfigVersion files
+set(CONF_INCLUDE_DIRS "${CMAKE_INSTALL_PREFIX}/include")
+configure_file(GUDHIConfig.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake" @ONLY)
+configure_file(GUDHIConfigVersion.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake" @ONLY)
+
+#---------------------------------------------------------------------------------------
+
+#---------------------------------------------------------------------------------------
+# Gudhi installation part
+
+# Install the GUDHIConfig.cmake and GUDHIConfigVersion.cmake
+install(FILES
+  "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake"
+  "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake"
+  DESTINATION share/gudhi)
+
+# install the include file on "make install"
+install(DIRECTORY include/gudhi DESTINATION include)
+#---------------------------------------------------------------------------------------
diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index 64429baa..ca2e47c1 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -5,6 +5,10 @@ find_package(Qt5 COMPONENTS Widgets Xml OpenGL)
 find_package(QGLViewer)
 find_package(OpenGL)
 
+if (CGAL_VERSION VERSION_EQUAL 4.8.0)
+  message(ERROR " GudhUI does not compile with CGAL 4.8.0. 4.8.1, 4.8.2 and 4.9 are OK.")
+endif()
+
 if (NOT CGAL_FOUND)
   message(ERROR " GudhUI requires CGAL and will not be compiled.")
 endif()
@@ -23,7 +27,7 @@ endif()
 
 
 
-if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
+if ( CGAL_FOUND AND Qt5_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND AND NOT CGAL_VERSION VERSION_EQUAL 4.8.0)
 
   set(CMAKE_AUTOMOC ON)
   set(CMAKE_AUTOUIC ON)
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 20700d86..a6b698c3 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -81,28 +81,26 @@ if(CGAL_FOUND)
       ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.weights 2 0.45)
 
 
-  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-    if (EIGEN3_FOUND)
-      add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
-      target_link_libraries(alpha_complex_persistence
-          ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-
-      add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp)
-      target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-
-      add_executable(custom_persistence_sort custom_persistence_sort.cpp)
-      target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-
-      if (TBB_FOUND)
-        target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES})
-        target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES})
-        target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES})
-      endif(TBB_FOUND)
-      add_test(alpha_complex_persistence_2_0_45 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_persistence
-          ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -m 0.45 -p 2)
-      add_test(periodic_alpha_complex_3d_persistence_2_0 ${CMAKE_CURRENT_BINARY_DIR}/periodic_alpha_complex_3d_persistence
-          ${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off ${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt 2 0)
-      add_test(custom_persistence_sort ${CMAKE_CURRENT_BINARY_DIR}/custom_persistence_sort)
-    endif(EIGEN3_FOUND)
-  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+    add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
+    target_link_libraries(alpha_complex_persistence
+        ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+    add_executable(periodic_alpha_complex_3d_persistence periodic_alpha_complex_3d_persistence.cpp)
+    target_link_libraries(periodic_alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+
+    add_executable(custom_persistence_sort custom_persistence_sort.cpp)
+    target_link_libraries(custom_persistence_sort ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+
+    if (TBB_FOUND)
+      target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES})
+      target_link_libraries(periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES})
+      target_link_libraries(custom_persistence_sort ${TBB_LIBRARIES})
+    endif(TBB_FOUND)
+    add_test(alpha_complex_persistence_2_0_45 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_persistence
+        ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -m 0.45 -p 2)
+    add_test(periodic_alpha_complex_3d_persistence_2_0 ${CMAKE_CURRENT_BINARY_DIR}/periodic_alpha_complex_3d_persistence
+        ${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off ${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt 2 0)
+    add_test(custom_persistence_sort ${CMAKE_CURRENT_BINARY_DIR}/custom_persistence_sort)
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
 endif(CGAL_FOUND)
diff --git a/src/Spatial_searching/test/CMakeLists.txt b/src/Spatial_searching/test/CMakeLists.txt
index 2c685c72..bdc95e4a 100644
--- a/src/Spatial_searching/test/CMakeLists.txt
+++ b/src/Spatial_searching/test/CMakeLists.txt
@@ -10,16 +10,12 @@ if (GPROF_PATH)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
 endif()
 
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    if (EIGEN3_FOUND)
-      add_executable( Spatial_searching_test_Kd_tree_search test_Kd_tree_search.cpp )
-      target_link_libraries(Spatial_searching_test_Kd_tree_search 
-        ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable( Spatial_searching_test_Kd_tree_search test_Kd_tree_search.cpp )
+  target_link_libraries(Spatial_searching_test_Kd_tree_search
+    ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
-      add_test(Spatial_searching_test_Kd_tree_search ${CMAKE_CURRENT_BINARY_DIR}/Spatial_searching_test_Kd_tree_search
-      # XML format for Jenkins xUnit plugin 
-      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Spatial_searching_UT.xml --log_level=test_suite --report_level=no)
-    endif()
-  endif ()
-endif()
+  add_test(Spatial_searching_test_Kd_tree_search ${CMAKE_CURRENT_BINARY_DIR}/Spatial_searching_test_Kd_tree_search
+  # XML format for Jenkins xUnit plugin
+  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Spatial_searching_UT.xml --log_level=test_suite --report_level=no)
+endif ()
diff --git a/src/Subsampling/example/CMakeLists.txt b/src/Subsampling/example/CMakeLists.txt
index 0fd3335c..bb043297 100644
--- a/src/Subsampling/example/CMakeLists.txt
+++ b/src/Subsampling/example/CMakeLists.txt
@@ -1,21 +1,17 @@
 cmake_minimum_required(VERSION 2.6)
 project(Subsampling_examples)
 
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    if (EIGEN3_FOUND)
-      add_executable(Subsampling_example_pick_n_random_points example_pick_n_random_points.cpp)
-      add_executable(Subsampling_example_choose_n_farthest_points example_choose_n_farthest_points.cpp)
-      add_executable(Subsampling_example_custom_kernel example_custom_kernel.cpp)
-      add_executable(Subsampling_example_sparsify_point_set example_sparsify_point_set.cpp)
-      target_link_libraries(Subsampling_example_sparsify_point_set ${CGAL_LIBRARY})
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable(Subsampling_example_pick_n_random_points example_pick_n_random_points.cpp)
+  add_executable(Subsampling_example_choose_n_farthest_points example_choose_n_farthest_points.cpp)
+  add_executable(Subsampling_example_custom_kernel example_custom_kernel.cpp)
+  add_executable(Subsampling_example_sparsify_point_set example_sparsify_point_set.cpp)
+  target_link_libraries(Subsampling_example_sparsify_point_set ${CGAL_LIBRARY})
 
-      add_test(Subsampling_example_pick_n_random_points
-               ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_pick_n_random_points)
-      add_test(Subsampling_example_choose_n_farthest_points
-               ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_choose_n_farthest_points)
-      add_test(Subsampling_example_sparsify_point_set
-               ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_sparsify_point_set)
-    endif()
-  endif ()
-endif()
+  add_test(Subsampling_example_pick_n_random_points
+           ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_pick_n_random_points)
+  add_test(Subsampling_example_choose_n_farthest_points
+           ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_choose_n_farthest_points)
+  add_test(Subsampling_example_sparsify_point_set
+           ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_example_sparsify_point_set)
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Subsampling/test/CMakeLists.txt b/src/Subsampling/test/CMakeLists.txt
index 3a2fb649..5517fe9d 100644
--- a/src/Subsampling/test/CMakeLists.txt
+++ b/src/Subsampling/test/CMakeLists.txt
@@ -10,29 +10,25 @@ if (GPROF_PATH)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
 endif()
 
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    if (EIGEN3_FOUND)
-      add_executable( Subsampling_test_pick_n_random_points test_pick_n_random_points.cpp )
-      target_link_libraries(Subsampling_test_pick_n_random_points ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable( Subsampling_test_pick_n_random_points test_pick_n_random_points.cpp )
+  target_link_libraries(Subsampling_test_pick_n_random_points ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
-      add_executable( Subsampling_test_choose_n_farthest_points test_choose_n_farthest_points.cpp )
-      target_link_libraries(Subsampling_test_choose_n_farthest_points ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  add_executable( Subsampling_test_choose_n_farthest_points test_choose_n_farthest_points.cpp )
+  target_link_libraries(Subsampling_test_choose_n_farthest_points ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
-      add_executable(Subsampling_test_sparsify_point_set test_sparsify_point_set.cpp)
-      target_link_libraries(Subsampling_test_sparsify_point_set ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  add_executable(Subsampling_test_sparsify_point_set test_sparsify_point_set.cpp)
+  target_link_libraries(Subsampling_test_sparsify_point_set ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 
-      add_test(Subsampling_test_pick_n_random_points ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_pick_n_random_points
-      # XML format for Jenkins xUnit plugin 
-      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_pick_n_random_points_UT.xml --log_level=test_suite --report_level=no)
+  add_test(Subsampling_test_pick_n_random_points ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_pick_n_random_points
+  # XML format for Jenkins xUnit plugin
+  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_pick_n_random_points_UT.xml --log_level=test_suite --report_level=no)
 
-      add_test(Subsampling_test_choose_n_farthest_points ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_choose_n_farthest_points
-      # XML format for Jenkins xUnit plugin 
-      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_choose_n_farthest_points_UT.xml --log_level=test_suite --report_level=no)
+  add_test(Subsampling_test_choose_n_farthest_points ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_choose_n_farthest_points
+  # XML format for Jenkins xUnit plugin
+  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_choose_n_farthest_points_UT.xml --log_level=test_suite --report_level=no)
 
-      add_test(Subsampling_test_sparsify_point_set ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_sparsify_point_set
-      # XML format for Jenkins xUnit plugin 
-      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_sparsify_point_set_UT.xml --log_level=test_suite --report_level=no)
-    endif()
-  endif ()
-endif()
+  add_test(Subsampling_test_sparsify_point_set ${CMAKE_CURRENT_BINARY_DIR}/Subsampling_test_sparsify_point_set
+  # XML format for Jenkins xUnit plugin
+  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Subsampling_test_sparsify_point_set_UT.xml --log_level=test_suite --report_level=no)
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Tangential_complex/benchmark/CMakeLists.txt b/src/Tangential_complex/benchmark/CMakeLists.txt
index 788c2b4d..ef772be8 100644
--- a/src/Tangential_complex/benchmark/CMakeLists.txt
+++ b/src/Tangential_complex/benchmark/CMakeLists.txt
@@ -1,17 +1,11 @@
 cmake_minimum_required(VERSION 2.6)
 project(Tangential_complex_benchmark)
 
-# need CGAL 4.8
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    if (EIGEN3_FOUND)
-      add_executable(Tangential_complex_benchmark benchmark_tc.cpp)
-      target_link_libraries(Tangential_complex_benchmark 
-        ${Boost_DATE_TIME_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-      if (TBB_FOUND)
-        target_link_libraries(Tangential_complex_benchmark ${TBB_LIBRARIES})
-      endif(TBB_FOUND)
-    endif(EIGEN3_FOUND)
-  endif (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-endif(CGAL_FOUND)
-
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable(Tangential_complex_benchmark benchmark_tc.cpp)
+  target_link_libraries(Tangential_complex_benchmark
+    ${Boost_DATE_TIME_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(Tangential_complex_benchmark ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Tangential_complex/example/CMakeLists.txt b/src/Tangential_complex/example/CMakeLists.txt
index a75ccd5b..47a56e3b 100644
--- a/src/Tangential_complex/example/CMakeLists.txt
+++ b/src/Tangential_complex/example/CMakeLists.txt
@@ -1,23 +1,19 @@
 cmake_minimum_required(VERSION 2.6)
 project(Tangential_complex_examples)
 
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    if (EIGEN3_FOUND)
-      add_executable( Tangential_complex_example_basic example_basic.cpp )
-      target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY})
-      add_executable( Tangential_complex_example_with_perturb example_with_perturb.cpp )
-      target_link_libraries(Tangential_complex_example_with_perturb ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY})
-      if (TBB_FOUND)
-        target_link_libraries(Tangential_complex_example_basic ${TBB_LIBRARIES})
-        target_link_libraries(Tangential_complex_example_with_perturb ${TBB_LIBRARIES})
-      endif(TBB_FOUND)
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable( Tangential_complex_example_basic example_basic.cpp )
+  target_link_libraries(Tangential_complex_example_basic ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY})
+  add_executable( Tangential_complex_example_with_perturb example_with_perturb.cpp )
+  target_link_libraries(Tangential_complex_example_with_perturb ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(Tangential_complex_example_basic ${TBB_LIBRARIES})
+    target_link_libraries(Tangential_complex_example_with_perturb ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
 
-      add_test(Tangential_complex_example_basic
-               ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_basic)
+  add_test(Tangential_complex_example_basic
+           ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_basic)
 
-      add_test(Tangential_complex_example_with_perturb
-               ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_with_perturb)
-    endif(EIGEN3_FOUND)
-  endif(NOT CGAL_VERSION VERSION_LESS 4.8.0)
-endif(CGAL_FOUND)
+  add_test(Tangential_complex_example_with_perturb
+           ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_example_with_perturb)
+endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Tangential_complex/test/CMakeLists.txt b/src/Tangential_complex/test/CMakeLists.txt
index 075028c8..b2bf5dd7 100644
--- a/src/Tangential_complex/test/CMakeLists.txt
+++ b/src/Tangential_complex/test/CMakeLists.txt
@@ -10,22 +10,14 @@ if (GPROF_PATH)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
 endif()
 
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-    if (EIGEN3_FOUND)
-      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
-      include( ${EIGEN3_USE_FILE} )
-      include_directories (BEFORE "../../include")
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable( Tangential_complex_test_TC test_tangential_complex.cpp )
+  target_link_libraries(Tangential_complex_test_TC ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(Tangential_complex_test_TC ${TBB_LIBRARIES})
+  endif()
+  add_test(Tangential_complex_test_TC ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_test_TC
+  # XML format for Jenkins xUnit plugin
+  --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Tangential_complex_UT.xml --log_level=test_suite --report_level=no)
 
-      add_executable( Tangential_complex_test_TC test_tangential_complex.cpp )
-      target_link_libraries(Tangential_complex_test_TC ${CGAL_LIBRARY} ${Boost_DATE_TIME_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
-      if (TBB_FOUND)
-        target_link_libraries(Tangential_complex_test_TC ${TBB_LIBRARIES})
-      endif()
-      add_test(Tangential_complex_test_TC ${CMAKE_CURRENT_BINARY_DIR}/Tangential_complex_test_TC
-      # XML format for Jenkins xUnit plugin 
-      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Tangential_complex_UT.xml --log_level=test_suite --report_level=no)
-
-    endif()
-  endif ()
-endif()
\ No newline at end of file
+endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index 9990c541..549a85be 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -9,40 +9,36 @@ endif()
 add_test(Witness_complex_test_nearest_landmark_table Witness_complex_example_nearest_landmark_table)
 
 # CGAL and Eigen3 are required for Euclidean version of Witness
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    if (EIGEN3_FOUND)
-      add_executable( Witness_complex_example_off example_witness_complex_off.cpp )
-      target_link_libraries(Witness_complex_example_off ${Boost_SYSTEM_LIBRARY})
-      add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp )
-      target_link_libraries(Witness_complex_example_strong_off ${Boost_SYSTEM_LIBRARY})
-      add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp )
-      target_link_libraries(Witness_complex_example_sphere ${Boost_SYSTEM_LIBRARY})
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+  add_executable( Witness_complex_example_off example_witness_complex_off.cpp )
+  target_link_libraries(Witness_complex_example_off ${Boost_SYSTEM_LIBRARY})
+  add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp )
+  target_link_libraries(Witness_complex_example_strong_off ${Boost_SYSTEM_LIBRARY})
+  add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp )
+  target_link_libraries(Witness_complex_example_sphere ${Boost_SYSTEM_LIBRARY})
 
-      add_executable ( Witness_complex_example_witness_persistence example_witness_complex_persistence.cpp )
-      target_link_libraries(Witness_complex_example_witness_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  add_executable ( Witness_complex_example_witness_persistence example_witness_complex_persistence.cpp )
+  target_link_libraries(Witness_complex_example_witness_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
-      add_executable ( Witness_complex_example_strong_witness_persistence example_strong_witness_persistence.cpp )
-      target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  add_executable ( Witness_complex_example_strong_witness_persistence example_strong_witness_persistence.cpp )
+  target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
-      if (TBB_FOUND)
-        target_link_libraries(Witness_complex_example_witness_persistence ${TBB_LIBRARIES})
-        target_link_libraries(Witness_complex_example_strong_witness_persistence ${TBB_LIBRARIES})
-      endif()
+  if (TBB_FOUND)
+    target_link_libraries(Witness_complex_example_witness_persistence ${TBB_LIBRARIES})
+    target_link_libraries(Witness_complex_example_strong_witness_persistence ${TBB_LIBRARIES})
+  endif()
 
-      add_test(Witness_complex_off_test_torus
-               ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_off
-               ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 20 1.0 3)
-      add_test(Witness_complex_strong_off_test_torus
-               ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_strong_off
-               ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 20 1.0 3)
-      add_test(Witness_complex_test_sphere_10 Witness_complex_example_sphere 10)
-      add_test(Witness_complex_test_torus_persistence
-               ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_witness_persistence
-               ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -l 20 -a 0.5)
-      add_test(Witness_complex_strong_test_torus_persistence
-               ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_strong_witness_persistence
-               ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -l 20 -a 0.5)
-    endif(EIGEN3_FOUND)
-  endif (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-endif()
+  add_test(Witness_complex_off_test_torus
+           ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_off
+           ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 20 1.0 3)
+  add_test(Witness_complex_strong_off_test_torus
+           ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_strong_off
+           ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 20 1.0 3)
+  add_test(Witness_complex_test_sphere_10 Witness_complex_example_sphere 10)
+  add_test(Witness_complex_test_torus_persistence
+           ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_witness_persistence
+           ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -l 20 -a 0.5)
+  add_test(Witness_complex_strong_test_torus_persistence
+           ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_example_strong_witness_persistence
+           ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off -l 20 -a 0.5)
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/src/Witness_complex/test/CMakeLists.txt b/src/Witness_complex/test/CMakeLists.txt
index 12b3be56..e73f9c3a 100644
--- a/src/Witness_complex/test/CMakeLists.txt
+++ b/src/Witness_complex/test/CMakeLists.txt
@@ -23,20 +23,16 @@ add_test(NAME simple_witness_complex
     --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Witness_complex_test_simple_witness_complexUT.xml --log_level=test_suite --report_level=no)
 
 # CGAL and Eigen3 are required for Euclidean version of Witness
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    if (EIGEN3_FOUND)
-      add_executable ( Witness_complex_test_euclidean_simple_witness_complex test_euclidean_simple_witness_complex.cpp )
-      target_link_libraries(Witness_complex_test_euclidean_simple_witness_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
-      if (TBB_FOUND)
-        target_link_libraries(Witness_complex_test_euclidean_simple_witness_complex ${TBB_LIBRARIES})
-      endif(TBB_FOUND)
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
+  add_executable ( Witness_complex_test_euclidean_simple_witness_complex test_euclidean_simple_witness_complex.cpp )
+  target_link_libraries(Witness_complex_test_euclidean_simple_witness_complex ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(Witness_complex_test_euclidean_simple_witness_complex ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
 
-      # Unitary tests definition and xml result file generation
-      add_test(NAME euclidean_simple_witness_complex
-        COMMAND ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_test_euclidean_simple_witness_complex
-          # XML format for Jenkins xUnit plugin
-          --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Witness_complex_test_euclidean_simple_witness_complexUT.xml --log_level=test_suite --report_level=no)
-    endif(EIGEN3_FOUND)
-  endif (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-endif()
+  # Unitary tests definition and xml result file generation
+  add_test(NAME euclidean_simple_witness_complex
+    COMMAND ${CMAKE_CURRENT_BINARY_DIR}/Witness_complex_test_euclidean_simple_witness_complex
+      # XML format for Jenkins xUnit plugin
+      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/Witness_complex_test_euclidean_simple_witness_complexUT.xml --log_level=test_suite --report_level=no)
+endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.txt b/src/cmake/modules/GUDHI_third_party_libraries.txt
new file mode 100644
index 00000000..75f73537
--- /dev/null
+++ b/src/cmake/modules/GUDHI_third_party_libraries.txt
@@ -0,0 +1,107 @@
+# This files manage third party libraries required by GUDHI
+
+find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework chrono timer date_time program_options thread REQUIRED)
+
+if(NOT Boost_FOUND)
+  message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.")
+endif(NOT Boost_FOUND)
+
+find_package(GMP)
+if(GMP_FOUND)
+  message(STATUS "GMP_LIBRARIES = ${GMP_LIBRARIES}")
+  INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
+  find_package(GMPXX)
+  if(GMPXX_FOUND)
+    message(STATUS "GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
+    INCLUDE_DIRECTORIES(${GMPXX_INCLUDE_DIR})
+  endif()
+endif()
+
+# In CMakeLists.txt, when include(${CGAL_USE_FILE}), CMAKE_CXX_FLAGS are overwritten.
+# cf. http://doc.cgal.org/latest/Manual/installation.html#title40
+# A workaround is to include(${CGAL_USE_FILE}) before adding "-std=c++11".
+# A fix would be to use https://cmake.org/cmake/help/v3.1/prop_gbl/CMAKE_CXX_KNOWN_FEATURES.html
+# or even better https://cmake.org/cmake/help/v3.1/variable/CMAKE_CXX_STANDARD.html
+# but it implies to use cmake version 3.1 at least.
+find_package(CGAL)
+
+# Only CGAL versions > 4.4 supports what Gudhi uses from CGAL
+if (CGAL_VERSION VERSION_LESS 4.4.0)
+  message("CGAL version ${CGAL_VERSION} is considered too old to be used by Gudhi.")
+  unset(CGAL_FOUND)
+endif()
+if(CGAL_FOUND)
+  message(STATUS "CGAL version: ${CGAL_VERSION}.")
+  include( ${CGAL_USE_FILE} )
+
+  if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
+    # HACK to detect CGAL version 4.8.0
+    # CGAL version 4.8, 4.8.1 and 4.8.2 are identified as version 4.8.1000)
+    # cf. https://github.com/CGAL/cgal/issues/1559
+    # Limit the HACK between CGAL versions 4.8 and 4.9 because of file read
+    if (NOT CGAL_VERSION VERSION_GREATER 4.9.0)
+      foreach(CGAL_INCLUDE_DIR ${CGAL_INCLUDE_DIRS})
+        if (EXISTS "${CGAL_INCLUDE_DIR}/CGAL/version.h")
+          FILE(READ "${CGAL_INCLUDE_DIR}/CGAL/version.h" contents)
+          STRING(REGEX REPLACE "\n" ";" contents "${contents}")
+          foreach(Line ${contents})
+            if("${Line}" STREQUAL "#define CGAL_VERSION 4.8")
+              set(CGAL_VERSION 4.8.0)
+              message (">>>>> HACK CGAL version to ${CGAL_VERSION}")
+            endif("${Line}" STREQUAL "#define CGAL_VERSION 4.8")
+          endforeach(Line ${contents})
+        endif (EXISTS "${CGAL_INCLUDE_DIR}/CGAL/version.h")
+      endforeach(CGAL_INCLUDE_DIR ${CGAL_INCLUDE_DIRS})
+    endif(NOT CGAL_VERSION VERSION_GREATER 4.9.0)
+
+    # For dev version
+    include_directories(BEFORE "src/common/include/gudhi_patches")
+    # For user version
+    include_directories(BEFORE "include/gudhi_patches")
+  endif()
+endif()
+
+# Find TBB package for parallel sort - not mandatory, just optional.
+set(TBB_FIND_QUIETLY ON)
+find_package(TBB)
+if (TBB_FOUND)
+  include(${TBB_USE_FILE})
+  message("TBB found in ${TBB_LIBRARY_DIRS}")
+  add_definitions(-DGUDHI_USE_TBB)
+endif()
+
+set(CGAL_WITH_EIGEN3_VERSION 0.0.0)
+find_package(Eigen3 3.1.0)
+if (EIGEN3_FOUND)
+  message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
+  include( ${EIGEN3_USE_FILE} )
+  set(CGAL_WITH_EIGEN3_VERSION ${CGAL_VERSION})
+endif (EIGEN3_FOUND)
+
+# Required programs for unitary tests purpose
+FIND_PROGRAM( GCOVR_PATH gcovr )
+if (GCOVR_PATH)
+  message("gcovr found in ${GCOVR_PATH}")
+endif()
+# Required programs for unitary tests purpose
+FIND_PROGRAM( GPROF_PATH gprof )
+if (GPROF_PATH)
+  message("gprof found in ${GPROF_PATH}")
+endif()
+FIND_PROGRAM( DIFF_PATH diff )
+if (DIFF_PATH)
+  message("diff found in ${DIFF_PATH}")
+endif()
+
+# BOOST ISSUE result_of vs C++11
+add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE)
+# BOOST ISSUE with Libraries name resolution under Windows
+add_definitions(-DBOOST_ALL_NO_LIB)
+# problem with Visual Studio link on Boost program_options
+add_definitions( -DBOOST_ALL_DYN_LINK )
+
+INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
+LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
+
+message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
+message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 593faea5..e6f29fa8 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -122,7 +122,7 @@
       <b>Author:</b> Cl&eacute;ment Jamin<br>
       <b>Introduced in:</b> GUDHI 2.0.0<br>
       <b>Copyright:</b> GPL v3<br>
-      <b>Requires:</b> \ref cgal &ge; 4.8.0 and \ref eigen3
+      <b>Requires:</b> \ref cgal &ge; 4.8.1 and \ref eigen3
     </td>
     <td width="75%">
     A Tangential Delaunay complex is a <a target="_blank" href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complex</a>
@@ -161,7 +161,7 @@
       <b>Author:</b> Fran&ccedil;ois Godi<br>
       <b>Introduced in:</b> GUDHI 2.0.0<br>
       <b>Copyright:</b> GPL v3<br>
-      <b>Requires:</b> \ref cgal &ge; 4.8.0 and \ref eigen3
+      <b>Requires:</b> \ref cgal &ge; 4.8.1 and \ref eigen3
     </td>
     <td width="75%">
     Bottleneck distance measures the similarity between two persistence diagrams. 
@@ -297,11 +297,27 @@ make doxygen
  * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
  * Persistent_cohomology/custom_persistence_sort.cpp</a>
  * 
- * The following example requires CGAL version &ge; 4.8.0:
- * \li <a href="_bottleneck_distance_2_bottleneck_basic_example_8cpp-example.html">
+ * The following example requires CGAL version &ge; 4.8.1:
+ * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
+ * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a>
+ * \li <a href="_bottleneck_distance_2bottleneck_basic_example_8cpp-example.html">
  * Bottleneck_distance/bottleneck_basic_example.cpp</a>
- * \li <a href="_bottleneck_distance_2_bottleneck_read_file_example_8cpp-example.html">
+ * \li <a href="_bottleneck_distance_2bottleneck_read_file_example_8cpp-example.html">
  * Bottleneck_distance/bottleneck_read_file_example.cpp</a>
+ * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html">
+ * Spatial_searching/example_spatial_searching.cpp</a>
+ * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html">
+ * Subsampling/example_choose_n_farthest_points.cpp</a>
+ * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html">
+ * Subsampling/example_custom_kernel.cpp</a>
+ * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html">
+ * Subsampling/example_pick_n_random_points.cpp</a>
+ * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html">
+ * Subsampling/example_sparsify_point_set.cpp</a>
+ * \li <a href="_tangential_complex_2example_basic_8cpp-example.html">
+ * Tangential_complex/example_basic.cpp</a>
+ * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html">
+ * Tangential_complex/example_with_perturb.cpp</a>
  *
  * \subsection eigen3 Eigen3
  * The \ref alpha_complex data structure and few examples requires
@@ -405,6 +421,7 @@ make doxygen
 /*! @file Examples
  * @example Alpha_complex/Alpha_complex_from_off.cpp
  * @example Alpha_complex/Alpha_complex_from_points.cpp
+ * @example Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp
  * @example Bottleneck_distance/bottleneck_basic_example.cpp
  * @example Bottleneck_distance/bottleneck_read_file_example.cpp
  * @example Bitmap_cubical_complex/Bitmap_cubical_complex.cpp
@@ -437,6 +454,11 @@ make doxygen
  * @example Skeleton_blocker/Skeleton_blocker_from_simplices.cpp
  * @example Skeleton_blocker/Skeleton_blocker_iteration.cpp
  * @example Skeleton_blocker/Skeleton_blocker_link.cpp
+ * @example Spatial_searching/example_spatial_searching.cpp
+ * @example Subsampling/example_choose_n_farthest_points.cpp
+ * @example Subsampling/example_custom_kernel.cpp
+ * @example Subsampling/example_pick_n_random_points.cpp
+ * @example Subsampling/example_sparsify_point_set.cpp
  * @example Tangential_complex/example_basic.cpp
  * @example Tangential_complex/example_with_perturb.cpp
  * @example Witness_complex/example_nearest_landmark_table.cpp
diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt
index b0c6d69a..61c94391 100644
--- a/src/common/example/CMakeLists.txt
+++ b/src/common/example/CMakeLists.txt
@@ -10,12 +10,10 @@ if(CGAL_FOUND)
   target_link_libraries(cgal_3D_off_reader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
   add_test(cgal_3D_off_reader ${CMAKE_CURRENT_BINARY_DIR}/cgal_3D_off_reader ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
 
-  # need CGAL 4.7
-  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-    if (EIGEN3_FOUND)
-      add_executable ( cgal_off_reader example_CGAL_points_off_reader.cpp )
-      target_link_libraries(cgal_off_reader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-      add_test(cgal_off_reader ${CMAKE_CURRENT_BINARY_DIR}/cgal_off_reader ${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off)
-    endif(EIGEN3_FOUND)
-  endif (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+  # need CGAL 4.7and Eigen3
+  if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
+    add_executable ( cgal_off_reader example_CGAL_points_off_reader.cpp )
+    target_link_libraries(cgal_off_reader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+    add_test(cgal_off_reader ${CMAKE_CURRENT_BINARY_DIR}/cgal_off_reader ${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off)
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
 endif()
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 25cf952e..2131505d 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -90,21 +90,16 @@ if(PYTHON_PATH AND CYTHON_PATH)
     file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/")
 
     if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-        # If CGAL_VERSION >= 4.8.1, include subsampling
-        # CGAL things are done in CGAL_VERSION >= 4.8.0
-        set(GUDHI_CYTHON_SUBSAMPLING "include 'cython/subsampling.pyx'")
+      # If CGAL_VERSION >= 4.8.1, include subsampling
+      set(GUDHI_CYTHON_SUBSAMPLING "include 'cython/subsampling.pyx'")
+      set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include 'cython/tangential_complex.pyx'")
+      set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include 'cython/bottleneck_distance.pyx'")
     else (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-      # Remove alpha complex unitary tests
+      # Remove subsampling unitary tests
       file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_subsampling.py)
       file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_ref.rst")
       file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_sum.rst")
       file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/subsampling_user.rst")
-    endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
-    if (NOT CGAL_VERSION VERSION_LESS 4.8.0)
-      # If CGAL_VERSION >= 4.8.0, include tangential complex
-      set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include 'cython/tangential_complex.pyx'")
-      set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include 'cython/bottleneck_distance.pyx'")
-    else (NOT CGAL_VERSION VERSION_LESS 4.8.0)
       # Remove tangential complex and bottleneck unitary tests
       file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_tangential_complex.py)
       file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/test/test_bottleneck_distance.py)
@@ -114,7 +109,7 @@ if(PYTHON_PATH AND CYTHON_PATH)
       file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_ref.rst")
       file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_sum.rst")
       file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/doc/tangential_complex_user.rst")
-    endif (NOT CGAL_VERSION VERSION_LESS 4.8.0)
+    endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
     if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
       # If CGAL_VERSION >= 4.7.0, include alpha
       set(GUDHI_CYTHON_ALPHA_COMPLEX "include 'cython/alpha_complex.pyx'")