Merge last trunk modification

Fix doc issue
Still doc issue


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1739 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0a99345f06e93a3525691699a6fe1505979e8e8e

1 files changed, 36 insertions, 56 deletions

diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 5fb4ba12..758bd6b1 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -30,17 +30,13 @@ endif()
 
 add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology)
 add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0)
-add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 3 -m 100)
-add_test(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_via_boundary_matrix ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.txt -r 0.3 -d 3 -p 3 -m 100)
-add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 2 -m 0)
-add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100)
+add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.16 -d 3 -p 3 -m 100)
+add_test(rips_persistence_via_boundary_matrix_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence_via_boundary_matrix ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.16 -d 3 -p 3 -m 100)
+add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 2 -m 0)
+add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/filtered_simplicial_complex/bunny_5000_complex.fsc -p 3 -m 100)
    
 if(GMP_FOUND)
-   message("GMP_LIBRARIES = ${GMP_LIBRARIES}")
-
    if(GMPXX_FOUND)
-      message("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
-
       add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
       target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
       add_executable ( performance_rips_persistence performance_rips_persistence.cpp )
@@ -52,53 +48,37 @@ if(GMP_FOUND)
 
    add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 2 -q 71 -m 100)
    endif(GMPXX_FOUND)
-else()
-  # message(WARNING "GMP not found.")
 endif(GMP_FOUND)
 
-  if(CGAL_FOUND)
-    add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
-    target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-
-    if (TBB_FOUND)
-      target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES})
-    endif(TBB_FOUND)
-    add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off 2 0.45)
-
-
-    if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
-      message(STATUS "CGAL version: ${CGAL_VERSION}.")
-
-      find_package(Eigen3 3.1.0)
-      if (EIGEN3_FOUND)
-        message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
-        include( ${EIGEN3_USE_FILE} )
-
-        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)
-
-      else()
-        message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
-      endif(EIGEN3_FOUND)
-    else()
-      message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
-    endif ()
-  else()
-    # message(WARNING "CGAL not found.")
-  endif(CGAL_FOUND)
-   
+if(CGAL_FOUND)
+  add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
+  target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+
+  if (TBB_FOUND)
+    target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
+  add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off 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)
+endif(CGAL_FOUND)