From c972b77524faec5d6f297d442539f65b9351654e Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 13 Nov 2015 16:41:12 +0000
Subject: Utils.h -> Debug_utils.h More verbose in debug mode (use NDEBUG
 instead of DEBUG_TRACES) GUDHI_CHECK function to throw in debug or ignore in
 release mode

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@911 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 250dc0c0f5146f0b9e3fce0e9a8ca0da6af7cf98
---
 src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h                   | 2 +-
 .../include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h       | 2 +-
 .../Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h  | 2 +-
 src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h           | 2 +-
 src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h | 2 +-
 src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h      | 2 +-
 src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp                | 2 +-
 7 files changed, 7 insertions(+), 7 deletions(-)

(limited to 'src/Skeleton_blocker')

diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
index 3be480fd..20df93eb 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
@@ -31,7 +31,7 @@
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h>
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h>
 
-#include <gudhi/Utils.h>  // xxx
+#include <gudhi/Debug_utils.h>
 
 namespace Gudhi {
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
index b33b9606..1b1fe3f0 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
@@ -25,7 +25,7 @@
 
 #include <gudhi/Skeleton_blocker_complex.h>
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h>
-#include <gudhi/Utils.h>
+#include <gudhi/Debug_utils.h>
 
 #include <map>
 #include <vector>
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h
index 4d71b3f5..27411fc1 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h
@@ -25,7 +25,7 @@
 #include <gudhi/Skeleton_blocker_link_complex.h>
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h>
 #include <gudhi/Skeleton_blocker/internal/Trie.h>
-#include <gudhi/Utils.h>
+#include <gudhi/Debug_utils.h>
 
 #include <boost/iterator/iterator_facade.hpp>
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
index d26d12b0..dc2d9e29 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
@@ -33,7 +33,7 @@
 #include <gudhi/Skeleton_blocker/internal/Top_faces.h>
 #include <gudhi/Skeleton_blocker/internal/Trie.h>
 
-#include <gudhi/Utils.h>
+#include <gudhi/Debug_utils.h>
 
 #include <boost/graph/adjacency_list.hpp>
 #include <boost/graph/connected_components.hpp>
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
index b8395251..3725b7a2 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
@@ -22,9 +22,9 @@
 #ifndef SKELETON_BLOCKER_GEOMETRIC_COMPLEX_H_
 #define SKELETON_BLOCKER_GEOMETRIC_COMPLEX_H_
 
-#include <gudhi/Utils.h>
 #include <gudhi/Skeleton_blocker_complex.h>
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h>
+#include <gudhi/Debug_utils.h>
 
 namespace Gudhi {
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h
index 95d8fa97..3d0039a1 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h
@@ -22,8 +22,8 @@
 #ifndef SKELETON_BLOCKER_LINK_COMPLEX_H_
 #define SKELETON_BLOCKER_LINK_COMPLEX_H_
 
-#include <gudhi/Utils.h>
 #include <gudhi/Skeleton_blocker_complex.h>
+#include <gudhi/Debug_utils.h>
 
 namespace Gudhi {
 
diff --git a/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp b/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp
index 319e3c43..d56a5c91 100644
--- a/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp
+++ b/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp
@@ -24,7 +24,7 @@
 #include <string>
 #include <fstream>
 #include <sstream>
-#include "gudhi/Utils.h"
+#include "gudhi/Debug_utils.h"
 #include "gudhi/Test.h"
 #include "gudhi/Skeleton_blocker.h"
 //#include "gudhi/Skeleton_blocker_link_complex.h"
-- 
cgit v1.2.3


From c85b24f7e0c489093e0c5ccca934eb53fafab623 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 4 Feb 2016 16:11:42 +0000
Subject: CMake strategy modification

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Win64_Boost_Xunit_fix@1003 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c917934525e020b54b2f4506b5c9d060a28c9d89
---
 CMakeLists.txt                                | 105 +++++++++++++++-----------
 data/points/generator/CMakeLists.txt          |  16 ----
 src/Bottleneck/test/CMakeLists.txt            |   4 -
 src/CMakeLists.txt                            |  67 ++++++++++------
 src/GudhUI/CMakeLists.txt                     |  20 -----
 src/Persistent_cohomology/test/CMakeLists.txt |   4 -
 src/Simplex_tree/example/CMakeLists.txt       |  17 -----
 src/Simplex_tree/test/CMakeLists.txt          |   4 -
 src/Skeleton_blocker/test/CMakeLists.txt      |   4 -
 9 files changed, 105 insertions(+), 136 deletions(-)

(limited to 'src/Skeleton_blocker')

diff --git a/CMakeLists.txt b/CMakeLists.txt
index edf7e63f..8ced7b0d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -7,52 +7,71 @@ configure_file(GUDHIVersion.cmake.in "${PROJECT_BINARY_DIR}/GUDHIVersion.cmake"
 
 find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework chrono timer program_options thread REQUIRED)
 
-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 = ${CMAKE_MODULE_PATH}")
-
-enable_testing()
-
-if(MSVC)
-  # Turn off some VC++ warnings
-  SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4267 /wd4668 /wd4311 /wd4800 /wd4820 /wd4503 /wd4244 /wd4345 /wd4996 /wd4396 /wd4018")
-else()
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O2 -std=c++11 -Wall -Wpedantic -Wsign-compare")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0")	
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}")
-endif()
-
-set(Boost_USE_STATIC_LIBS        ON)
-set(Boost_USE_MULTITHREADED      ON)
-set(Boost_USE_STATIC_RUNTIME    OFF)
-
-find_package(GMP)
-if(GMP_FOUND)
-	find_package(GMPXX)
-endif()
-
-find_package(CGAL)
-
-# Find TBB package for parallel sort - not mandatory, just optional.
-set(TBB_FIND_QUIETLY ON)
-find_package(TBB)
-
-# 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 ${GPROF_PATH}")
-endif()
-
-
 if(NOT Boost_FOUND)
   message(FATAL_ERROR "NOTICE: This demo requires Boost and will not be compiled.")
 else()
+
+  set(CMAKE_PREFIX_PATH "${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 = ${CMAKE_MODULE_PATH}")
+
+  enable_testing()
+
+  find_package(GMP)
+  if(GMP_FOUND)
+    INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
+    find_package(GMPXX)
+    if(GMPXX_FOUND)
+      INCLUDE_DIRECTORIES(${GMPXX_INCLUDE_DIR})
+    endif()
+  endif()
+
+  # find CGAL package before set of CXX flags because
+  # in CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
+  # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
+  set(CGAL_DONT_OVERRIDE_CMAKE_FLAGS TRUE CACHE BOOL "Force CGAL to maintain CMAKE flags")
+  find_package(CGAL)
+  if(CGAL_FOUND)
+    include( ${CGAL_USE_FILE} )
+    set(CMAKE_CXX_CGAL_FOR_GUDHI_FLAGS "-frounding-math")
+  endif()
+  
+  if(MSVC)
+    # Turn off some VC++ warnings
+    set(CMAKE_CXX_FLAGS "${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 -Wpedantic -Wsign-compare ${CMAKE_CXX_CGAL_FOR_GUDHI_FLAGS}")
+    set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb -O0")	
+    # set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}")
+  endif()
+
+  if(CMAKE_BUILD_TYPE MATCHES Debug)
+    message("Compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}")
+  else()
+    message("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)
+
+  # 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()
+
+
   # BOOST ISSUE result_of vs C++11
   add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE)
   # BOOST ISSUE with Libraries name resolution under Windows
diff --git a/data/points/generator/CMakeLists.txt b/data/points/generator/CMakeLists.txt
index 26b44446..c01a380d 100644
--- a/data/points/generator/CMakeLists.txt
+++ b/data/points/generator/CMakeLists.txt
@@ -5,22 +5,6 @@ if(CGAL_FOUND)
   if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
     message(STATUS "CGAL version: ${CGAL_VERSION}.")
 
-    include( ${CGAL_USE_FILE} )
-    # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
-    # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
-    # A workaround is to add "-std=c++11" again.
-    # 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.
-    if(NOT MSVC)
-      include(CheckCXXCompilerFlag)
-      CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
-      if(COMPILER_SUPPORTS_CXX11)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-      endif()
-    endif()
-    # - End of workaround
-
     find_package(Eigen3 3.1.0)
     if (EIGEN3_FOUND)
       include( ${EIGEN3_USE_FILE} )
diff --git a/src/Bottleneck/test/CMakeLists.txt b/src/Bottleneck/test/CMakeLists.txt
index 3dfd80cd..ad63c080 100644
--- a/src/Bottleneck/test/CMakeLists.txt
+++ b/src/Bottleneck/test/CMakeLists.txt
@@ -4,14 +4,10 @@ project(GUDHIBottleneckUT)
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
 endif()
 if (GPROF_PATH)
   # for gprof to make coverage reports - Jenkins
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
 endif()
 
 add_executable ( BottleneckUT bottleneck_unit_test.cpp )
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 3c38483c..a67e7c92 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -9,33 +9,52 @@ list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/modules/")
 
 find_package(Boost REQUIRED COMPONENTS system filesystem program_options chrono timer REQUIRED)
 
-if (NOT CMAKE_BUILD_TYPE)
- set(CMAKE_BUILD_TYPE "Release")
-endif()
-if(MSVC)
-  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")
-endif()
-
-set(Boost_USE_STATIC_LIBS        ON)
-set(Boost_USE_MULTITHREADED      ON)
-set(Boost_USE_STATIC_RUNTIME    OFF)
-
-find_package(GMP)
-if(GMP_FOUND)
-  find_package(GMPXX)
-endif()
-
-find_package(CGAL)
-
-# Find TBB package for parallel sort - not mandatory, just optional.
-set(TBB_FIND_QUIETLY ON)
-find_package(TBB)
-
 if(NOT Boost_FOUND)
   message(FATAL_ERROR "NOTICE: This demo requires Boost and will not be compiled.")
 else()
+
+  find_package(GMP)
+  if(GMP_FOUND)
+    INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
+    find_package(GMPXX)
+    if(GMPXX_FOUND)
+      INCLUDE_DIRECTORIES(${GMPXX_INCLUDE_DIR})
+    endif()
+  endif()
+
+  # find CGAL package before set of CXX flags because
+  # in CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
+  # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
+  set(CGAL_DONT_OVERRIDE_CMAKE_FLAGS TRUE CACHE BOOL "Force CGAL to maintain CMAKE flags")
+  find_package(CGAL)
+  if(CGAL_FOUND)
+    include( ${CGAL_USE_FILE} )
+    set(CMAKE_CXX_CGAL_FOR_GUDHI_FLAGS "-frounding-math")
+  endif()
+
+  if (NOT CMAKE_BUILD_TYPE)
+    set(CMAKE_BUILD_TYPE "Release")
+  endif()
+  if(MSVC)
+    set(CMAKE_CXX_FLAGS "${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 ${CMAKE_CXX_CGAL_FOR_GUDHI_FLAGS}")
+  endif()
+
+  if(CMAKE_BUILD_TYPE MATCHES Debug)
+    message("Compilation flags are: ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}")
+  else()
+    message("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)
+
   # BOOST ISSUE result_of vs C++11
   add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE)
   # BOOST ISSUE with Libraries name resolution under Windows
diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index 71f4fd1a..1ee43d91 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -1,7 +1,6 @@
 cmake_minimum_required(VERSION 2.8)
 project(GudhUI)
 
-find_package(CGAL  COMPONENTS Qt4)
 find_package(Qt4)
 find_package(QGLViewer)
 find_package(OpenGL)
@@ -14,27 +13,8 @@ if ( CGAL_FOUND AND QT4_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
   SET(Boost_USE_STATIC_LIBS ON)
   SET(Boost_USE_MULTITHREAD OFF)
 
-  INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
-  LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
-  
   include(${QT_USE_FILE})
 
-  include(${CGAL_USE_FILE})
-  # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
-  # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
-  # A workaround is to add "-std=c++11" again.
-  # 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.
-  if(NOT MSVC)
-    include(CheckCXXCompilerFlag)
-    CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
-    if(COMPILER_SUPPORTS_CXX11)
-      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-    endif()
-  endif()
-  # - End of workaround
-
   include_directories (${QGLVIEWER_INCLUDE_DIR})
   include_directories(.)	
  
diff --git a/src/Persistent_cohomology/test/CMakeLists.txt b/src/Persistent_cohomology/test/CMakeLists.txt
index ed63a6ac..d16be5be 100644
--- a/src/Persistent_cohomology/test/CMakeLists.txt
+++ b/src/Persistent_cohomology/test/CMakeLists.txt
@@ -4,14 +4,10 @@ project(GUDHIPersistentCohomologyUT)
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")	
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
 endif()
 if (GPROF_PATH)
   # for gprof to make coverage reports - Jenkins
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
 endif()
 
 add_executable ( PersistentCohomologyUT persistent_cohomology_unit_test.cpp )
diff --git a/src/Simplex_tree/example/CMakeLists.txt b/src/Simplex_tree/example/CMakeLists.txt
index a86b99a1..200161a6 100644
--- a/src/Simplex_tree/example/CMakeLists.txt
+++ b/src/Simplex_tree/example/CMakeLists.txt
@@ -14,23 +14,6 @@ add_test(mini_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/mini_simplex_tree)
 
 # An example with Simplex-tree using CGAL alpha_shapes_3
 if(GMP_FOUND AND CGAL_FOUND)
-  include( ${CGAL_USE_FILE} )
-  # In CMakeLists.txt, when include(${CGAL_USE_FILE}), CXX_FLAGS are overwritten.
-  # cf. http://doc.cgal.org/latest/Manual/installation.html#title40
-  # A workaround is to add "-std=c++11" again.
-  # 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.
-  if(NOT MSVC)
-    include(CheckCXXCompilerFlag)
-    CHECK_CXX_COMPILER_FLAG(-std=c++11 COMPILER_SUPPORTS_CXX11)
-    if(COMPILER_SUPPORTS_CXX11)
-      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-    endif()
-  endif()
-  # - End of workaround
-
-  INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR})
   add_executable ( simplex_tree_from_alpha_shapes_3 simplex_tree_from_alpha_shapes_3.cpp )
   target_link_libraries(simplex_tree_from_alpha_shapes_3 ${GMP_LIBRARIES} ${CGAL_LIBRARY} ${Boost_SYSTEM_LIBRARY})
   add_test(simplex_tree_from_alpha_shapes_3 ${CMAKE_CURRENT_BINARY_DIR}/simplex_tree_from_alpha_shapes_3 ${CMAKE_SOURCE_DIR}/data/points/bunny_5000)
diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt
index c9eae163..1f2f7d33 100644
--- a/src/Simplex_tree/test/CMakeLists.txt
+++ b/src/Simplex_tree/test/CMakeLists.txt
@@ -4,14 +4,10 @@ project(GUDHISimplexTreeUT)
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")	
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
 endif()
 if (GPROF_PATH)
   # for gprof to make coverage reports - Jenkins
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
 endif()
 
 add_executable ( SimplexTreeUT simplex_tree_unit_test.cpp )
diff --git a/src/Skeleton_blocker/test/CMakeLists.txt b/src/Skeleton_blocker/test/CMakeLists.txt
index 8b6fb672..5e063845 100644
--- a/src/Skeleton_blocker/test/CMakeLists.txt
+++ b/src/Skeleton_blocker/test/CMakeLists.txt
@@ -4,14 +4,10 @@ project(GUDHIskbl)
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")	
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
 endif()
 if (GPROF_PATH)
   # for gprof to make coverage reports - Jenkins
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
 endif()
 
 add_executable(TestSkeletonBlockerComplex TestSkeletonBlockerComplex.cpp)
-- 
cgit v1.2.3


From 001f501ffa371fc810d4f24812d26845bd61f349 Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 30 Mar 2016 10:43:10 +0000
Subject: Add cubical complex to main page Homogeneize the author/copyright
 sections of modules Exclude data and GudhUI from doxygen

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Doxygen_for_GUDHI_1.3.0@1085 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 1b89161f3253553a02935885334b2fc6cf58055e
---
 src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h    |  3 ++-
 .../include/gudhi/Bitmap_cubical_complex.h                    | 11 ++++-------
 .../include/gudhi/Bitmap_cubical_complex/counter.h            |  2 +-
 .../include/gudhi/Bitmap_cubical_complex_base.h               |  7 ++-----
 ...Bitmap_cubical_complex_periodic_boundary_conditions_base.h |  6 ++----
 src/Contraction/include/gudhi/Edge_contraction.h              |  1 -
 src/Doxyfile                                                  |  3 ++-
 .../include/gudhi/Persistent_cohomology.h                     |  6 +-----
 src/Simplex_tree/include/gudhi/Simplex_tree.h                 |  5 +----
 src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h         |  1 -
 src/common/doc/main_page.h                                    |  4 ++--
 11 files changed, 17 insertions(+), 32 deletions(-)

(limited to 'src/Skeleton_blocker')

diff --git a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
index be4caaad..83921427 100644
--- a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
+++ b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
@@ -145,7 +145,8 @@ namespace Cubical_complex {
 
  * \section BitmapExamples Examples
  * End user programs are available in example/Bitmap_cubical_complex folder.
-
+ * 
+ * \copyright GNU General Public License v3.
  */
 /** @} */  // end defgroup cubical_complex
 
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
index 67e1fed3..54ae47d0 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex.h
@@ -46,18 +46,15 @@ const bool globalDbg = false;
 template <typename T> class is_before_in_filtration;
 
 /**
- * This is a Bitmap_cubical_complex class. It joints a functionalities of Bitmap_cubical_complex_base and
+ * @class Bitmap_cubical_complex Bitmap_cubical_complex.h gudhi/Bitmap_cubical_complex.h
+ * @brief Cubical complex represented as a bitmap.
+ * @ingroup cubical_complex
+ * @details This is a Bitmap_cubical_complex class. It joints a functionalities of Bitmap_cubical_complex_base and
  * Bitmap_cubical_complex_periodic_boundary_conditions_base classes into
  * Gudhi persistent homology engine. It is a template class that inherit from its template parameter. The template
  * parameter is supposed to be either Bitmap_cubical_complex_base or
  * Bitmap_cubical_complex_periodic_boundary_conditions_base class.
  **/
-
-/**
- *@class Bitmap_cubical_complex
- *@brief Cubical complex represented as a bitmap.
- *@ingroup cubical_complex
- */
 template <typename T>
 class Bitmap_cubical_complex : public T {
  public:
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h
index 266ce051..bee19344 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex/counter.h
@@ -31,6 +31,7 @@ namespace Gudhi {
 namespace Cubical_complex {
 
 /**
+ * @class counter counter.h gudhi/Bitmap_cubical_complex/counter.h
  * This is an implementation of a counter being a vector of integers. 
  * The constructor of the class takes as an input two vectors W and V. 
  * It assumes that W < V coordinatewise.
@@ -40,7 +41,6 @@ namespace Cubical_complex {
  * The current counter reach the end counter V if the value returned by the increment function is FALSE.
  * This class is needed for the implementation of a bitmapCubicalComplex.
  **/
-
 class counter {
  public:
   /**
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
index 7294da98..4bdc94ef 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
@@ -39,13 +39,10 @@ namespace Gudhi {
 namespace Cubical_complex {
 
 /**
- * @class Bitmap_cubical_complex_base
+ * @class Bitmap_cubical_complex_base Bitmap_cubical_complex_base.h gudhi/Bitmap_cubical_complex_base.h
  * @brief Cubical complex represented as a bitmap, class with basic implementation.
  * @ingroup cubical_complex
- */
-
-/**
- * This is a class implementing a basic bitmap data structure to store cubical complexes.
+ * @details This is a class implementing a basic bitmap data structure to store cubical complexes.
  * It implements only the most basic subroutines.
  * The idea of the bitmap is the following. Our aim is to have a memory efficient
  * data structure to store d-dimensional cubical complex
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h
index a446c0e8..5b7e4115 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h
@@ -39,12 +39,10 @@ namespace Cubical_complex {
 // the cells on the right / top are not in the Bitmap_cubical_complex_periodic_boundary_conditions_base
 
 /**
- * @class Bitmap_cubical_complex_periodic_boundary_conditions_base
+ * @class Bitmap_cubical_complex_periodic_boundary_conditions_base Bitmap_cubical_complex_periodic_boundary_conditions_base.h gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h
  * @brief Cubical complex with periodic boundary conditions represented as a bitmap.
  * @ingroup cubical_complex
- */
-/**
- * This is a class implementing a bitmap data structure with periodic boundary conditions. Most of the functions are
+ * @details This is a class implementing a bitmap data structure with periodic boundary conditions. Most of the functions are
  * identical to the functions from Bitmap_cubical_complex_base.
  * The ones that needed to be updated are the constructors and get_boundary_of_a_cell and get_coboundary_of_a_cell.
  */
diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h
index 73236db9..1fe563d6 100644
--- a/src/Contraction/include/gudhi/Edge_contraction.h
+++ b/src/Contraction/include/gudhi/Edge_contraction.h
@@ -226,7 +226,6 @@ Time to simplify and enumerate simplices:
 
 
 \copyright GNU General Public License v3.                         
-\verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
 */
 /** @} */  // end defgroup
 }  // namespace contraction
diff --git a/src/Doxyfile b/src/Doxyfile
index 8fe41755..f7fba3e6 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -779,7 +779,8 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = 
+EXCLUDE                = data/ \
+	GudhUI/
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index 3c331f0f..1b86f1f9 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -48,6 +48,7 @@ namespace persistent_cohomology {
 
 /** \defgroup persistent_cohomology Persistent Cohomology
   *
+ \author    Clément Maria
 
   Computation of persistent cohomology using the algorithm of 
    \cite DBLP:journals/dcg/SilvaMV11 and \cite DBLP:journals/corr/abs-1208-5018 
@@ -169,11 +170,6 @@ points sampling a Klein bottle in \f$\mathbb{R}^5\f$ with a simplex tree, its co
 Hasse diagram and the computation of persistent homology and multi-field persistent homology for the 
 different representations.
 
-
-
- \author    Clément Maria
- \version   1.0
- \date      2014
  \copyright GNU General Public License v3.
  @{  
  */
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 46670b85..ba09db63 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -48,6 +48,7 @@
 namespace Gudhi {
 
 /** \defgroup simplex_tree Filtered Complexes
+ * \author    Cl&eacute;ment Maria
  *
  * A simplicial complex \f$\mathbf{K}\f$
  * on a set of vertices \f$V = \{1, \cdots ,|V|\}\f$ is a collection of simplices
@@ -75,10 +76,6 @@ namespace Gudhi {
  when accessing the boundary of a simplex, but is less compact and harder to construct from
  scratch.
 
-
- * \author    Clément Maria
- * \version   1.0
- * \date      2014
  * \copyright GNU General Public License v3.
  * @{
  */
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
index 615b3a81..74c6a71d 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
@@ -240,7 +240,6 @@ their collaboration to write the two initial papers
 
 
 \copyright GNU General Public License v3.                         
-\verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
 */
 /** @} */  // end defgroup
 
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 56cb82bb..6f3d8603 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -41,7 +41,7 @@
 <table border="0">
   <tr>
     <td width="25%">
-      <b>Author:</b> Clément Maria<br>
+      <b>Author:</b> Cl&eacute;ment Maria<br>
       <b>Introduced in:</b> GUDHI 1.0.0<br>
       <b>Copyright:</b> GPL v3<br>
     </td>
@@ -114,7 +114,7 @@
 <table border="0">
   <tr>
     <td width="25%">
-      <b>Author:</b> Clément Maria<br>
+      <b>Author:</b> Cl&eacute;ment Maria<br>
       <b>Introduced in:</b> GUDHI 1.0.0<br>
       <b>Copyright:</b> GPL v3<br>
     </td>
-- 
cgit v1.2.3