Merge remote-tracking branch 'upstream/master' into cech_opti

7 files changed, 43 insertions, 23 deletions

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 8023e04c..f9f77ef7 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -12,8 +12,12 @@ set(GUDHI_MISSING_MODULES "" CACHE INTERNAL "GUDHI_MISSING_MODULES")
 # This variable is used by Cython CMakeLists.txt and by GUDHI_third_party_libraries to know its path
 set(GUDHI_PYTHON_PATH "python")
 
-# For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH
-include(GUDHI_third_party_libraries NO_POLICY_SCOPE)
+include(GUDHI_submodules)
+
+if (WITH_GUDHI_THIRD_PARTY)
+  # For third parties libraries management - To be done last as CGAL updates CMAKE_MODULE_PATH
+  include(GUDHI_third_party_libraries NO_POLICY_SCOPE)
+endif()
 
 include(GUDHI_compilation_flags)
 
@@ -67,7 +71,9 @@ foreach(GUDHI_MODULE ${GUDHI_MODULES})
   endforeach()
 endforeach()
 
-add_subdirectory(GudhUI)
+if (WITH_GUDHI_THIRD_PARTY)
+  add_subdirectory(GudhUI)
+endif()
 
 message("++ GUDHI_MODULES list is:\"${GUDHI_MODULES}\"")
 message("++ GUDHI_MISSING_MODULES list is:\"${GUDHI_MISSING_MODULES}\"")
diff --git a/src/Cech_complex/include/gudhi/Cech_complex_blocker.h b/src/Cech_complex/include/gudhi/Cech_complex_blocker.h
index 47b6c5e3..543f677e 100644
--- a/src/Cech_complex/include/gudhi/Cech_complex_blocker.h
+++ b/src/Cech_complex/include/gudhi/Cech_complex_blocker.h
@@ -74,6 +74,8 @@ class Cech_blocker {
     CGAL::NT_converter<FT, Filtration_value> cast_to_fv;
     Filtration_value radius = 0;
     bool is_min_enclos_ball = false;
+    Point_cloud points;
+    points.reserve(sc_ptr_->dimension(sh)+1);
 
     // for each face of simplex sh, test outsider point is indeed inside enclosing ball, if yes, take it and exit loop, otherwise, new sphere is circumsphere of all vertices
     for (auto face_opposite_vertex : sc_ptr_->boundary_opposite_vertex_simplex_range(sh)) {
@@ -83,9 +85,8 @@ class Cech_blocker {
             sph_key = k;
         }
         else {
-            Point_cloud face_points;
             for (auto vertex : sc_ptr_->simplex_vertex_range(face_opposite_vertex.first)) {
-                face_points.push_back(cc_ptr_->get_point(vertex));
+                points.push_back(cc_ptr_->get_point(vertex));
 #ifdef DEBUG_TRACES
                 std::clog << "#(" << vertex << ")#";
 #endif  // DEBUG_TRACES
@@ -93,9 +94,9 @@ class Cech_blocker {
             // Put edge sphere in cache
             sc_ptr_->assign_key(face_opposite_vertex.first, cc_ptr_->get_cache().size());
             sph_key = cc_ptr_->get_cache().size();
-            cc_ptr_->get_cache().push_back(get_sphere(face_points.cbegin(), face_points.cend()));
-            // Clear face_points
-            face_points.clear();
+            cc_ptr_->get_cache().push_back(get_sphere(points.cbegin(), points.cend()));
+            // Clear face points
+            points.clear();
         }
         // Check if the minimal enclosing ball of current face contains the extra point/opposite vertex
         if (kernel_.squared_distance_d_object()(cc_ptr_->get_cache()[sph_key].first, cc_ptr_->get_point(face_opposite_vertex.second)) <= cc_ptr_->get_cache()[sph_key].second) {
@@ -113,7 +114,6 @@ class Cech_blocker {
     }
     // Spheres of each face don't contain the whole simplex
     if(!is_min_enclos_ball) {
-        Point_cloud points;
         for (auto vertex : sc_ptr_->simplex_vertex_range(sh)) {
             points.push_back(cc_ptr_->get_point(vertex));
         }
diff --git a/src/Doxyfile.in b/src/Doxyfile.in
index d0fad45f..6e0e0333 100644
--- a/src/Doxyfile.in
+++ b/src/Doxyfile.in
@@ -152,7 +152,7 @@ FULL_PATH_NAMES        = YES
 # will be relative from the directory where doxygen is started.
 # This tag requires that the tag FULL_PATH_NAMES is set to YES.
 
-STRIP_FROM_PATH        =
+STRIP_FROM_PATH        = @CMAKE_SOURCE_DIR@
 
 # The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
 # path mentioned in the documentation of a class, which tells the reader which
@@ -162,7 +162,8 @@ STRIP_FROM_PATH        =
 # using the -I flag.
 
 STRIP_FROM_INC_PATH    = include \
-                         concept
+                         concept \
+                         @CMAKE_SOURCE_DIR@
 
 # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
 # less readable) file names. This can be useful is your file systems doesn't
@@ -711,7 +712,7 @@ CITE_BIB_FILES         = @CMAKE_SOURCE_DIR@/biblio/bibliography.bib \
 # messages are off.
 # The default value is: NO.
 
-QUIET                  = NO
+QUIET                  = YES
 
 # The WARNINGS tag can be used to turn on/off the warning messages that are
 # generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
@@ -765,7 +766,7 @@ WARN_FORMAT            = "$file:$line: $text"
 # messages should be written. If left blank the output is written to standard
 # error (stderr).
 
-WARN_LOGFILE           =
+WARN_LOGFILE           = doxygen.log
 
 #---------------------------------------------------------------------------
 # Configuration options related to the input files
@@ -832,7 +833,7 @@ EXCLUDE                = @CMAKE_SOURCE_DIR@/data/ \
                          @CMAKE_SOURCE_DIR@/ext/ \
                          @CMAKE_SOURCE_DIR@/README.md \
                          @CMAKE_SOURCE_DIR@/.github \
-                         @CMAKE_CURRENT_BINARY_DIR@/new_gudhi_version_creation.md \
+                         @CMAKE_CURRENT_BINARY_DIR@ \
                          @GUDHI_DOXYGEN_SOURCE_PREFIX@/GudhUI/ \
                          @GUDHI_DOXYGEN_SOURCE_PREFIX@/cmake/ \
                          @GUDHI_DOXYGEN_SOURCE_PREFIX@/python/
diff --git a/src/cmake/modules/GUDHI_options.cmake b/src/cmake/modules/GUDHI_options.cmake
index c75b72f5..5e28c87d 100644
--- a/src/cmake/modules/GUDHI_options.cmake
+++ b/src/cmake/modules/GUDHI_options.cmake
@@ -4,3 +4,12 @@ option(WITH_GUDHI_REMOTE_TEST "Activate/deactivate datasets fetching test which
 option(WITH_GUDHI_PYTHON "Activate/deactivate python module compilation and installation" ON)
 option(WITH_GUDHI_TEST "Activate/deactivate examples compilation and installation" ON)
 option(WITH_GUDHI_UTILITIES "Activate/deactivate utilities compilation and installation" ON)
+option(WITH_GUDHI_THIRD_PARTY "Activate/deactivate third party libraries cmake detection. When set to OFF, it is usefull for doxygen or user_version i.e." ON)
+
+if (NOT WITH_GUDHI_THIRD_PARTY)
+  set (WITH_GUDHI_BENCHMARK OFF)
+  set (WITH_GUDHI_EXAMPLE OFF)
+  set (WITH_GUDHI_PYTHON OFF)
+  set (WITH_GUDHI_TEST OFF)
+  set (WITH_GUDHI_UTILITIES OFF)
+endif()
\ No newline at end of file
diff --git a/src/cmake/modules/GUDHI_submodules.cmake b/src/cmake/modules/GUDHI_submodules.cmake
new file mode 100644
index 00000000..78b045bd
--- /dev/null
+++ b/src/cmake/modules/GUDHI_submodules.cmake
@@ -0,0 +1,5 @@
+# For those who dislike bundled dependencies, this indicates where to find a preinstalled Hera.
+set(HERA_WASSERSTEIN_INTERNAL_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/wasserstein/include)
+set(HERA_WASSERSTEIN_INCLUDE_DIR ${HERA_WASSERSTEIN_INTERNAL_INCLUDE_DIR} CACHE PATH "Directory where one can find Hera's wasserstein.h")
+set(HERA_BOTTLENECK_INTERNAL_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/bottleneck/include)
+set(HERA_BOTTLENECK_INCLUDE_DIR ${HERA_BOTTLENECK_INTERNAL_INCLUDE_DIR} CACHE PATH "Directory where one can find Hera's bottleneck.h")
\ No newline at end of file
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 6ba822ad..2cf6787e 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -48,12 +48,6 @@ if(CGAL_FOUND)
   include( ${CGAL_USE_FILE} )
 endif()
 
-# For those who dislike bundled dependencies, this indicates where to find a preinstalled Hera.
-set(HERA_WASSERSTEIN_INTERNAL_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/wasserstein/include)
-set(HERA_WASSERSTEIN_INCLUDE_DIR ${HERA_WASSERSTEIN_INTERNAL_INCLUDE_DIR} CACHE PATH "Directory where one can find Hera's wasserstein.h")
-set(HERA_BOTTLENECK_INTERNAL_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/bottleneck/include)
-set(HERA_BOTTLENECK_INCLUDE_DIR ${HERA_BOTTLENECK_INTERNAL_INCLUDE_DIR} CACHE PATH "Directory where one can find Hera's bottleneck.h")
-
 option(WITH_GUDHI_USE_TBB "Build with Intel TBB parallelization" ON)
 
 # Find TBB package for parallel sort - not mandatory, just optional.
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
index 229c9f59..28526498 100644
--- a/src/common/doc/installation.h
+++ b/src/common/doc/installation.h
@@ -43,12 +43,17 @@ make \endverbatim
  * Testing fetching datasets feature requires the use of the internet and is disabled by default. If you want to include this test, set WITH_GUDHI_REMOTE_TEST to ON when building in the previous step (note that this test is included in the python module):
  * \verbatim cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_REMOTE_TEST=ON --DWITH_GUDHI_PYTHON=ON .. \endverbatim
  * 
- * \subsection documentationgeneration Documentation
- * To generate the documentation, <a target="_blank" href="http://www.doxygen.org/">Doxygen</a> is required.
- * Run the following command in a terminal:
+ * \subsection documentationgeneration C++ documentation
+ * To generate the C++ documentation, the <a target="_blank" href="http://www.doxygen.org/">doxygen</a> program
+ * is required (version &ge; 1.9.3 is advised). Run the following command in a terminal:
  * \verbatim make doxygen \endverbatim
  * Documentation will be generated in a folder named <code>html</code>.
  *
+ * In case there is not a full setup present and only the documentation should be build the following command sequence
+ * can be used:
+\verbatim  cmake -DWITH_GUDHI_THIRD_PARTY=OFF ..
+make doxygen\endverbatim
+ *
  * \subsection helloworld Hello world !
  * The <a target="_blank" href="https://github.com/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.