Bottleneck does not require Eigen3 (C++ and Python)

Doc issue about examples requiring Eigen3



git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2666 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5e127d4e8137a44ee3bd688c32653acfb4a55007

5 files changed, 54 insertions, 26 deletions

diff --git a/src/Bottleneck_distance/benchmark/CMakeLists.txt b/src/Bottleneck_distance/benchmark/CMakeLists.txt
index 170081ce..20a4e47b 100644
--- a/src/Bottleneck_distance/benchmark/CMakeLists.txt
+++ b/src/Bottleneck_distance/benchmark/CMakeLists.txt
@@ -1,9 +1,9 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_benchmark)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+if (NOT CGAL_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)
+endif(NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index dc1da31c..eac617db 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -1,30 +1,38 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_examples)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+if (NOT CGAL_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_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
-  target_link_libraries(alpha_rips_persistence_bottleneck_distance ${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(NAME Bottleneck_distance_example_basic COMMAND $<TARGET_FILE:bottleneck_basic_example>)
 
-  add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck
-      COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance>
-      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3")
-
   add_test(NAME Bottleneck_read_file_example
       COMMAND $<TARGET_FILE:bottleneck_read_file_example>
       "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers")
 
   install(TARGETS bottleneck_read_file_example DESTINATION bin)
   install(TARGETS bottleneck_basic_example DESTINATION bin)
-  install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin)
 
+endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+
+# Eigen3 and CGAL > 4.7.0 is required for alpha complex
+# CGAL > 4.8.1 is required for bottleneck distance =>
+if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
+  target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
+  add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck
+           COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance>
+           "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3")
+
+  install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin)
+  if (TBB_FOUND)
+    target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
 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 a165d472..2676b82c 100644
--- a/src/Bottleneck_distance/test/CMakeLists.txt
+++ b/src/Bottleneck_distance/test/CMakeLists.txt
@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_tests)
 
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   include(GUDHI_test_coverage)
 
   add_executable ( Bottleneck_distance_test_unit bottleneck_unit_test.cpp )
@@ -12,4 +12,4 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
 
   gudhi_add_coverage_test(Bottleneck_distance_test_unit)
 
-endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index bd4615f5..1a7994a5 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -160,7 +160,7 @@
       <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; 4.8.1 and \ref eigen3
+      <b>Requires:</b> \ref cgal &ge; 4.8.1
     </td>
     <td width="75%">
     Bottleneck distance measures the similarity between two persistence diagrams. 
@@ -329,13 +329,29 @@ make doxygen
  * Alpha_complex/Alpha_complex_from_off.cpp</a>
  * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
  * Alpha_complex/Alpha_complex_from_points.cpp</a>
+ * \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="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
  * Persistent_cohomology/alpha_complex_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
  * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
  * Persistent_cohomology/custom_persistence_sort.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 tbb Threading Building Blocks
  * <a target="_blank" href="https://www.threadingbuildingblocks.org/">Intel&reg; TBB</a> lets you easily write parallel
  * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index db23d42b..baeeb203 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -73,10 +73,12 @@ if(CYTHON_FOUND)
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_EIGEN3_ENABLED', ")
   endif (EIGEN3_FOUND)
 
+  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+    set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
+  endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
     set(GUDHI_CYTHON_SUBSAMPLING "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/subsampling.pyx'")
     set(GUDHI_CYTHON_TANGENTIAL_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/tangential_complex.pyx'")
-    set(GUDHI_CYTHON_BOTTLENECK_DISTANCE "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/bottleneck_distance.pyx'")
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
     set(GUDHI_CYTHON_ALPHA_COMPLEX "include '${CMAKE_CURRENT_SOURCE_DIR}/cython/alpha_complex.pyx'")
@@ -157,22 +159,13 @@ if(CYTHON_FOUND)
 
   # Test examples
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-    # Bottleneck
+    # Bottleneck and Alpha
     add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
              -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
 
-    add_test(NAME bottleneck_basic_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
-
-    add_test(NAME test_bottleneck_distance_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py)
-
     # Tangential
     add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
@@ -190,6 +183,17 @@ if(CYTHON_FOUND)
              COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_subsampling.py)
 
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
+    # Bottleneck
+    add_test(NAME bottleneck_basic_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
+
+    add_test(NAME test_bottleneck_distance_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${PYTHON_EXECUTABLE} -m pytest ${CMAKE_CURRENT_SOURCE_DIR}/test/test_bottleneck_distance.py)
+  endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
 
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.7.0)
     # Alpha