GUDHI 2.0.1 as released by upstream in a tarball.upstream/2.0.1

3 files changed, 54 insertions, 22 deletions

diff --git a/cmake/modules/GUDHI_modules.cmake b/cmake/modules/GUDHI_modules.cmake
new file mode 100644
index 00000000..f95d0c34
--- /dev/null
+++ b/cmake/modules/GUDHI_modules.cmake
@@ -0,0 +1,41 @@
+# A function to add a new module in GUDHI
+
+set(GUDHI_MODULES "")
+set(GUDHI_MODULES_FULL_LIST "")
+function(add_gudhi_module file_path)
+  option("WITH_MODULE_GUDHI_${file_path}" "Activate/desactivate ${file_path} compilation and installation" ON)
+  if (WITH_MODULE_GUDHI_${file_path})
+    set(GUDHI_MODULES ${GUDHI_MODULES} ${file_path} PARENT_SCOPE)
+  endif()
+  # Required by user_version
+  set(GUDHI_MODULES_FULL_LIST ${GUDHI_MODULES_FULL_LIST} ${file_path} PARENT_SCOPE)
+  # Include module headers is independant - You may ask for no Alpha complex module but Python interface i.e.
+  if(IS_DIRECTORY ${CMAKE_SOURCE_DIR}/src/${file_path}/include/)
+    include_directories(src/${file_path}/include/)
+  endif()
+
+endfunction(add_gudhi_module)
+
+option(WITH_GUDHI_BENCHMARK "Activate/desactivate benchmark compilation" OFF)
+option(WITH_GUDHI_EXAMPLE "Activate/desactivate examples compilation and installation" OFF)
+option(WITH_GUDHI_PYTHON "Activate/desactivate python module compilation and installation" ON)
+option(WITH_GUDHI_TEST "Activate/desactivate examples compilation and installation" ON)
+option(WITH_GUDHI_UTILITIES "Activate/desactivate utilities compilation and installation" ON)
+
+if (WITH_GUDHI_BENCHMARK)
+  set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};benchmark")
+endif()
+if (WITH_GUDHI_EXAMPLE)
+  set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};example")
+endif()
+if (WITH_GUDHI_TEST)
+  set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};test")
+endif()
+if (WITH_GUDHI_UTILITIES)
+  set(GUDHI_SUB_DIRECTORIES "${GUDHI_SUB_DIRECTORIES};utilities")
+endif()
+
+message("++ GUDHI_SUB_DIRECTORIES list is:\"${GUDHI_SUB_DIRECTORIES}\"")
+
+
+
diff --git a/cmake/modules/GUDHI_third_party_libraries.cmake b/cmake/modules/GUDHI_third_party_libraries.cmake
index 5f84c602..f2bbafdc 100644
--- a/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -1,6 +1,6 @@
 # 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)
+find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework program_options thread)
 
 if(NOT Boost_FOUND)
   message(FATAL_ERROR "NOTICE: This program requires Boost and will not be compiled.")
@@ -99,6 +99,8 @@ add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE)
 add_definitions(-DBOOST_ALL_NO_LIB)
 # problem with Visual Studio link on Boost program_options
 add_definitions( -DBOOST_ALL_DYN_LINK )
+# problem on Mac with boost_system and boost_thread
+add_definitions( -DBOOST_SYSTEM_NO_DEPRECATED )
 
 INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
 LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
@@ -106,19 +108,6 @@ LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
 message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
 message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
 
-macro( find_the_lib placeholder THE_LIBS )
-  set (THE_LIB_WE_FOUND "NO")
-  foreach(THE_LIB ${THE_LIBS})
-    if(EXISTS ${THE_LIB})
-      get_filename_component(THE_LIB_WE ${THE_LIB} NAME_WE)
-      if (NOT THE_LIB_WE_FOUND)
-        set (THE_LIB_WE_FOUND "YES")
-        set(returnValue "${THE_LIB_WE}")
-      endif(NOT THE_LIB_WE_FOUND)
-    endif(EXISTS ${THE_LIB})
-  endforeach(THE_LIB ${THE_LIBS})
-endmacro( find_the_lib )
-
 # Find the correct Python interpreter.
 # Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 or -DPython_ADDITIONAL_VERSIONS=3 for instance.
 find_package(Cython)
@@ -128,17 +117,20 @@ if(NOT GUDHI_CYTHON_PATH)
 endif(NOT GUDHI_CYTHON_PATH)
 
 if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
-  # Unitary tests are available through py.test
-  find_program( PYTEST_PATH py.test )
   # Default found version 2
   if(PYTHON_VERSION_MAJOR EQUAL 2)
     # Documentation generation is available through sphinx
     find_program( SPHINX_PATH sphinx-build )
   elseif(PYTHON_VERSION_MAJOR EQUAL 3)
-    # Documentation generation is available through sphinx
-    set(SPHINX_PATH "${CMAKE_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build")
+    # No sphinx-build in Pyton3, just hack it
+    set(SPHINX_PATH "${PYTHON_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/${GUDHI_CYTHON_PATH}/doc/python3-sphinx-build.py")
   else()
     message(FATAL_ERROR "ERROR: Try to compile the Cython interface. Python version ${PYTHON_VERSION_STRING} is not valid.")
   endif(PYTHON_VERSION_MAJOR EQUAL 2)
+  # get PYTHON_SITE_PACKAGES relative path from a python command line
+  execute_process(
+    COMMAND "${PYTHON_EXECUTABLE}" -c "from distutils.sysconfig import get_python_lib; print (get_python_lib(prefix='', plat_specific=True))"
+    OUTPUT_VARIABLE PYTHON_SITE_PACKAGES
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
 endif(PYTHONINTERP_FOUND AND CYTHON_FOUND)
 
diff --git a/cmake/modules/GUDHI_user_version_target.txt b/cmake/modules/GUDHI_user_version_target.cmake
index ca6bcd34..cff64ad2 100644
--- a/cmake/modules/GUDHI_user_version_target.txt
+++ b/cmake/modules/GUDHI_user_version_target.cmake
@@ -47,11 +47,10 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
   add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                      copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI)
   
-  set(GUDHI_MODULES "common;Alpha_complex;Bitmap_cubical_complex;Bottleneck_distance;Contraction;Hasse_complex;Persistent_cohomology;Rips_complex;Simplex_tree;Skeleton_blocker;Spatial_searching;Subsampling;Tangential_complex;Witness_complex")
-  set(GUDHI_DIRECTORIES "doc;example;concept")
+  set(GUDHI_DIRECTORIES "doc;example;concept;utilities")
   set(GUDHI_INCLUDE_DIRECTORIES "include/gudhi;include/gudhi_patches")
 
-  foreach(GUDHI_MODULE ${GUDHI_MODULES})
+  foreach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
     foreach(GUDHI_DIRECTORY ${GUDHI_DIRECTORIES})
       # Find files
       file(GLOB GUDHI_FILES ${CMAKE_SOURCE_DIR}/src/${GUDHI_MODULE}/${GUDHI_DIRECTORY}/*)
@@ -86,6 +85,6 @@ if (NOT CMAKE_VERSION VERSION_LESS 2.8.11)
       endforeach()
     endforeach(GUDHI_INCLUDE_DIRECTORY ${GUDHI_INCLUDE_DIRECTORIES})
 
-  endforeach(GUDHI_MODULE ${GUDHI_MODULES})
+  endforeach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
 
 endif()