5 files changed, 40 insertions, 30 deletions
diff --git a/src/cmake/modules/GUDHI_boost_test.cmake b/src/cmake/modules/GUDHI_boost_test.cmake
new file mode 100644
index 00000000..c3b29883
--- /dev/null
+++ b/src/cmake/modules/GUDHI_boost_test.cmake
@@ -0,0 +1,26 @@
+if (WITH_GUDHI_BOOST_TEST_COVERAGE)
+  # Make CTest output XML coverage report - WITH_GUDHI_BOOST_TEST_COVERAGE must be set - default is OFF
+  if (GCOVR_PATH)
+    # for gcovr to make coverage reports - Corbera Jenkins plugin
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
+  endif()
+  if (GPROF_PATH)
+    # for gprof to make coverage reports - Jenkins
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
+  endif()
+  set(GUDHI_UT_LOG_FORMAT "--log_format=XML")
+  set(GUDHI_UT_LOG_SINK "--log_sink=${CMAKE_BINARY_DIR}/${unitary_test}_UT.xml")
+  set(GUDHI_UT_LOG_LEVEL "--log_level=test_suite")
+  set(GUDHI_UT_REPORT_LEVEL "--report_level=no")
+else (WITH_GUDHI_BOOST_TEST_COVERAGE)
+  # Make CTest more verbose and color output
+  set(GUDHI_UT_LOG_LEVEL "--color_output")
+  set(GUDHI_UT_REPORT_LEVEL "--report_level=detailed")
+endif(WITH_GUDHI_BOOST_TEST_COVERAGE)
+
+function(gudhi_add_boost_test unitary_test)
+  target_link_libraries(${unitary_test} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+  add_test(NAME ${unitary_test} COMMAND $<TARGET_FILE:${unitary_test}>
+      ${GUDHI_UT_LOG_FORMAT} ${GUDHI_UT_LOG_SINK}
+      ${GUDHI_UT_LOG_LEVEL} ${GUDHI_UT_REPORT_LEVEL})
+endfunction()
diff --git a/src/cmake/modules/GUDHI_compilation_flags.cmake b/src/cmake/modules/GUDHI_compilation_flags.cmake
index 6cd2614d..34c2e065 100644
--- a/src/cmake/modules/GUDHI_compilation_flags.cmake
+++ b/src/cmake/modules/GUDHI_compilation_flags.cmake
@@ -73,3 +73,5 @@ if(CMAKE_BUILD_TYPE MATCHES Debug)
 else()
   message("++ Release compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
 endif()
+
+option(WITH_GUDHI_BOOST_TEST_COVERAGE "Report xml coverage files on boost tests" OFF)
diff --git a/src/cmake/modules/GUDHI_test_coverage.cmake b/src/cmake/modules/GUDHI_test_coverage.cmake
deleted file mode 100644
index bea5b2d6..00000000
--- a/src/cmake/modules/GUDHI_test_coverage.cmake
+++ /dev/null
@@ -1,26 +0,0 @@
-
-if (GCOVR_PATH)
-  # for gcovr to make coverage reports - Corbera Jenkins plugin
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-endif()
-if (GPROF_PATH)
-  # for gprof to make coverage reports - Jenkins
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-endif()
-
-if (DEBUG_TRACES)
-  # Make CTest more verbose with DEBUG_TRACES - no XML output
-  set(GUDHI_UT_LOG_LEVEL "--log_level=all")
-  set(GUDHI_UT_REPORT_LEVEL "--report_level=detailed")
-else()
-  set(GUDHI_UT_LOG_FORMAT "--log_format=XML")
-  set(GUDHI_UT_LOG_SINK "--log_sink=${CMAKE_BINARY_DIR}/${unitary_test}_UT.xml")
-  set(GUDHI_UT_LOG_LEVEL "--log_level=test_suite")
-  set(GUDHI_UT_REPORT_LEVEL "--report_level=no")
-endif()
-
-function(gudhi_add_coverage_test unitary_test)
-  add_test(NAME ${unitary_test} COMMAND $<TARGET_FILE:${unitary_test}>
-      ${GUDHI_UT_LOG_FORMAT} ${GUDHI_UT_LOG_SINK}
-      ${GUDHI_UT_LOG_LEVEL} ${GUDHI_UT_REPORT_LEVEL})
-endfunction()
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 360a230b..24a34150 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -125,6 +125,8 @@ if( PYTHONINTERP_FOUND )
   find_python_module("numpy")
   find_python_module("scipy")
   find_python_module("sphinx")
+  find_python_module("sklearn")
+  find_python_module("ot")
 endif()
 
 if(NOT GUDHI_PYTHON_PATH)
diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake
index f75fb19e..4fa74330 100644
--- a/src/cmake/modules/GUDHI_user_version_target.cmake
+++ b/src/cmake/modules/GUDHI_user_version_target.cmake
@@ -18,12 +18,20 @@ foreach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
   set(GUDHI_DOXYGEN_IMAGE_PATH "${GUDHI_DOXYGEN_IMAGE_PATH}    doc/${GUDHI_MODULE}/ \\  \n")
 endforeach(GUDHI_MODULE ${GUDHI_MODULES_FULL_LIST})
 
-# Generate setup.py file to cythonize Gudhi - This file must be named setup.py by convention
+# Generate Doxyfile for Doxygen - cf. root CMakeLists.txt for explanation
 configure_file(${CMAKE_SOURCE_DIR}/src/Doxyfile.in "${CMAKE_CURRENT_BINARY_DIR}/src/Doxyfile" @ONLY)
-
 add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
         copy ${CMAKE_CURRENT_BINARY_DIR}/src/Doxyfile ${GUDHI_USER_VERSION_DIR}/Doxyfile)
 
+# Generate bib files for Doxygen - cf. root CMakeLists.txt for explanation
+string(TIMESTAMP GUDHI_VERSION_YEAR "%Y")
+configure_file(${CMAKE_SOURCE_DIR}/biblio/how_to_cite_gudhi.bib.in "${CMAKE_CURRENT_BINARY_DIR}/biblio/how_to_cite_gudhi.bib" @ONLY)
+file(COPY "${CMAKE_SOURCE_DIR}/biblio/how_to_cite_cgal.bib" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/biblio/")
+file(COPY "${CMAKE_SOURCE_DIR}/biblio/bibliography.bib" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/biblio/")
+# Copy biblio directory for user version
+add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
+                   copy_directory ${CMAKE_CURRENT_BINARY_DIR}/biblio ${GUDHI_USER_VERSION_DIR}/biblio)
+
 add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                    copy ${CMAKE_SOURCE_DIR}/Conventions.txt ${GUDHI_USER_VERSION_DIR}/Conventions.txt)
 add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
@@ -40,8 +48,6 @@ add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                    copy ${CMAKE_SOURCE_DIR}/CMakeGUDHIVersion.txt ${GUDHI_USER_VERSION_DIR}/CMakeGUDHIVersion.txt)
 
 add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                   copy_directory ${CMAKE_SOURCE_DIR}/biblio ${GUDHI_USER_VERSION_DIR}/biblio)
-add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                    copy_directory ${CMAKE_SOURCE_DIR}/${GUDHI_PYTHON_PATH} ${GUDHI_USER_VERSION_DIR}/python)
 add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                    copy_directory ${CMAKE_SOURCE_DIR}/data ${GUDHI_USER_VERSION_DIR}/data)