merge last trunk modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3908 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ab0fe69130ba3cbb329e0e975053809180edba5d

6 files changed, 55 insertions, 15 deletions

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index c60346d5..6c446104 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -71,7 +71,7 @@ export(PACKAGE GUDHI)
 
 message("++ make install will install ${PROJECT_NAME} in the following directory : ${CMAKE_INSTALL_PREFIX}")
 # Create the GUDHIConfig.cmake and GUDHIConfigVersion files
-set(CONF_INCLUDE_DIRS "${CMAKE_INSTALL_PREFIX}/include")
+set(CONF_INCLUDE_DIRS "${CMAKE_SOURCE_DIR}/include;${CMAKE_INSTALL_PREFIX}/include")
 configure_file(GUDHIConfig.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake" @ONLY)
 configure_file(GUDHIConfigVersion.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake" @ONLY)
 
diff --git a/src/GUDHIConfig.cmake.in b/src/GUDHIConfig.cmake.in
index 02b540dc..8d82f235 100644
--- a/src/GUDHIConfig.cmake.in
+++ b/src/GUDHIConfig.cmake.in
@@ -1,7 +1,12 @@
 # - Config file for the GUDHI package
 # It defines the following variables
 #  GUDHI_INCLUDE_DIRS - include directories for GUDHI
+#
+# Order is :
+# 1. user defined GUDHI_INCLUDE_DIRS
+# 2. ${CMAKE_SOURCE_DIR}/include     => Where the 'cmake' has been done
+# 3. ${CMAKE_INSTALL_PREFIX}/include => Where the 'make install' has been performed
 
 # Compute paths
-set(GUDHI_INCLUDE_DIRS "@CONF_INCLUDE_DIRS@")
+set(GUDHI_INCLUDE_DIRS "${GUDHI_INCLUDE_DIRS};@CONF_INCLUDE_DIRS@")
 
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index c68b5c0b..c51e47a5 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -300,7 +300,10 @@ class Persistent_cohomology {
     // with multiplicity. We used to sum the coefficients directly in
     // annotations_in_boundary by using a map, we now do it later.
     typedef std::pair<Column *, int> annotation_t;
-    thread_local std::vector<annotation_t> annotations_in_boundary;
+#ifdef GUDHI_CAN_USE_CXX11_THREAD_LOCAL
+    thread_local
+#endif  // GUDHI_CAN_USE_CXX11_THREAD_LOCAL
+    std::vector<annotation_t> annotations_in_boundary;
     annotations_in_boundary.clear();
     int sign = 1 - 2 * (dim_sigma % 2);  // \in {-1,1} provides the sign in the
                                          // alternate sum in the boundary.
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index ee96d5a2..3ab23c12 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -1057,7 +1057,10 @@ class Simplex_tree {
     Dictionary_it next = siblings->members().begin();
     ++next;
 
-    thread_local std::vector<std::pair<Vertex_handle, Node> > inter;
+#ifdef GUDHI_CAN_USE_CXX11_THREAD_LOCAL
+    thread_local
+#endif  // GUDHI_CAN_USE_CXX11_THREAD_LOCAL
+    std::vector<std::pair<Vertex_handle, Node> > inter;
     for (Dictionary_it s_h = siblings->members().begin();
          s_h != siblings->members().end(); ++s_h, ++next) {
       Simplex_handle root_sh = find_vertex(s_h->first);
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
index d36a216f..ab54cbc7 100644
--- a/src/common/doc/installation.h
+++ b/src/common/doc/installation.h
@@ -2,22 +2,34 @@
  *  \tableofcontents
  * As GUDHI is a header only library, there is no need to install the library.
  * 
- * Examples of GUDHI headers inclusion can be found in \ref demos.
+ * Examples of GUDHI headers inclusion can be found in \ref utilities.
  * 
  * \section compiling Compiling
  * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a>  &ge; 1.48.0
  * and <a target="_blank" href="https://www.cmake.org/">CMake</a> &ge; 3.1.
  * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015.
  * 
- * \subsection demos Demos and examples
- * To build the demos and examples, run the following commands in a terminal:
+ * \subsection utilities Utilities and examples
+ * To build the utilities, run the following commands in a terminal:
 \verbatim  cd /path-to-gudhi/
 mkdir build
 cd build/
 cmake ..
 make \endverbatim
- * A list of examples is available <a href="examples.html">here</a>.
+ * By default, examples are disabled. You can activate their compilation with
+ * <a href="https://cmake.org/cmake/help/v3.0/manual/ccmake.1.html">ccmake</a> (on Linux and Mac OSX),
+ * <a href="https://cmake.org/cmake/help/v3.0/manual/cmake-gui.1.html">cmake-gui</a> (on Windows) or y mofifying the
+ * cmake command as follows :
+\verbatim  cmake -DWITH_GUDHI_EXAMPLE=ON ..
+make \endverbatim
+ * A list of utilities and examples is available <a href="examples.html">here</a>.
  * 
+ * \subsection libraryinstallation Installation
+ * To install the library (headers and activated utilities), run the following command in a terminal:
+ * \verbatim  make install \endverbatim
+ * This action may require to be in the sudoer or administrator of the machine in function of the operating system and
+ * of <a href="https://cmake.org/cmake/help/v3.0/variable/CMAKE_INSTALL_PREFIX.html">CMAKE_INSTALL_PREFIX</a>.
+ *
  * \subsection testsuites Test suites
  * To test your build, run the following command in a terminal:
  * \verbatim  make test \endverbatim
@@ -31,6 +43,10 @@ make doxygen
 # You can customize the directory name by calling `cmake -DUSER_VERSION_DIR=/my/custom/folder`
 \endverbatim
  *
+ * \subsection helloworld Hello world !
+ * The <a target="_blank" href="https://gitlab.inria.fr/GUDHI/hello-gudhi-world">Hello world for GUDHI</a>
+ * project is an example to help developers to make their own C++ project on top of the GUDHI library.
+ *
  * \section optionallibrary Optional third-party library
  * \subsection gmp GMP
  * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 1849a6ec..09ea28f1 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -130,7 +130,11 @@ if(CYTHON_FOUND)
   if(CGAL_FOUND)
     can_cgal_use_cxx11_thread_local()
     if (NOT CGAL_CAN_USE_CXX11_THREAD_LOCAL_RESULT)
-      add_gudhi_cython_lib(${Boost_THREAD_LIBRARY})
+      if(CMAKE_BUILD_TYPE MATCHES Debug)
+        add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_DEBUG}")
+      else()
+        add_gudhi_cython_lib("${Boost_THREAD_LIBRARY_RELEASE}")
+      endif()
       set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
     endif()
     # Add CGAL compilation args
@@ -139,22 +143,26 @@ if(CYTHON_FOUND)
       set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_HEADER_ONLY', ")
     else(CGAL_HEADER_ONLY)
       add_gudhi_debug_info("CGAL version ${CGAL_VERSION}")
-      add_gudhi_cython_lib(${CGAL_LIBRARY})
+      add_gudhi_cython_lib("${CGAL_LIBRARY}")
       set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${CGAL_LIBRARIES_DIR}', ")
       # If CGAL is not header only, CGAL library may link with boost system,
-      add_gudhi_cython_lib(${Boost_SYSTEM_LIBRARY})
+      if(CMAKE_BUILD_TYPE MATCHES Debug)
+        add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_DEBUG}")
+      else()
+        add_gudhi_cython_lib("${Boost_SYSTEM_LIBRARY_RELEASE}")
+      endif()
       set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${Boost_LIBRARY_DIRS}', ")
     endif(CGAL_HEADER_ONLY)
     # GMP and GMPXX are not required, but if present, CGAL will link with them.
     if(GMP_FOUND)
       add_gudhi_debug_info("GMP_LIBRARIES = ${GMP_LIBRARIES}")
       set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMP', ")
-      add_gudhi_cython_lib(${GMP_LIBRARIES})
+      add_gudhi_cython_lib("${GMP_LIBRARIES}")
       set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMP_LIBRARIES_DIR}', ")
       if(GMPXX_FOUND)
         add_gudhi_debug_info("GMPXX_LIBRARIES = ${GMPXX_LIBRARIES}")
         set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DCGAL_USE_GMPXX', ")
-        add_gudhi_cython_lib(${GMPXX_LIBRARIES})
+        add_gudhi_cython_lib("${GMPXX_LIBRARIES}")
         set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${GMPXX_LIBRARIES_DIR}', ")
       endif(GMPXX_FOUND)
     endif(GMP_FOUND)
@@ -176,8 +184,13 @@ if(CYTHON_FOUND)
   if (TBB_FOUND AND WITH_GUDHI_USE_TBB)
     add_gudhi_debug_info("TBB version ${TBB_INTERFACE_VERSION} found and used")
     set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DGUDHI_USE_TBB', ")
-    add_gudhi_cython_lib(${TBB_RELEASE_LIBRARY})
-    add_gudhi_cython_lib(${TBB_MALLOC_RELEASE_LIBRARY})
+    if(CMAKE_BUILD_TYPE MATCHES Debug)
+      add_gudhi_cython_lib("${TBB_DEBUG_LIBRARY}")
+      add_gudhi_cython_lib("${TBB_MALLOC_DEBUG_LIBRARY}")
+    else()
+      add_gudhi_cython_lib("${TBB_RELEASE_LIBRARY}")
+      add_gudhi_cython_lib("${TBB_MALLOC_RELEASE_LIBRARY}")
+    endif()
     set(GUDHI_CYTHON_LIBRARY_DIRS "${GUDHI_CYTHON_LIBRARY_DIRS}'${TBB_LIBRARY_DIRS}', ")
     set(GUDHI_CYTHON_INCLUDE_DIRS "${GUDHI_CYTHON_INCLUDE_DIRS}'${TBB_INCLUDE_DIRS}', ")
   endif()