Merge pull request #641 from VincentRouvreau/doxygen_only

Doxygen only

10 files changed, 54 insertions, 24 deletions

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 90737006..e2df5c87 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -58,7 +58,7 @@ jobs:
             git submodule update
             mkdir build
             cd build
-            cmake -DUSER_VERSION_DIR=version ..
+            cmake -DWITH_GUDHI_THIRD_PARTY=OFF -DUSER_VERSION_DIR=version ..
             make user_version
             cd version
             cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 -DWITH_GUDHI_REMOTE_TEST=ON .
@@ -79,7 +79,7 @@ jobs:
 
   doxygen:
     docker:
-      - image: gudhi/ci_for_gudhi:latest
+      - image: gudhi/doxygen_for_gudhi:latest
     steps:
       - checkout
       - run:
@@ -89,15 +89,15 @@ jobs:
             git submodule update
             mkdir build
             cd build
-            cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF -DUSER_VERSION_DIR=version ..
+            cmake -DWITH_GUDHI_THIRD_PARTY=OFF -DUSER_VERSION_DIR=version ..
             make user_version
             cd version
             mkdir build
             cd build
-            cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF ..
-            make doxygen 2>&1 | tee dox.log
-            grep warning dox.log
-            cp dox.log html/
+            cmake -DWITH_GUDHI_THIRD_PARTY=OFF ..
+            make doxygen
+            grep warning doxygen.log
+            cp doxygen.log html/
             cp -R html /tmp/doxygen
 
       - store_artifacts:
diff --git a/.github/for_maintainers/tests_strategy.md b/.github/for_maintainers/tests_strategy.md
index 338d4282..d0ae76ef 100644
--- a/.github/for_maintainers/tests_strategy.md
+++ b/.github/for_maintainers/tests_strategy.md
@@ -4,6 +4,11 @@ This document tries to sum up the tests strategy that has been put in place for
 
 The aim is to help maintainers to anticipate third parties modifications, updates.
 
+## CMake options
+
+[CMake GUDHI options](../../src/cmake/modules/GUDHI_options.cmake) allows to activate/deactivate what should be built and tested.
+Note the special option `WITH_GUDHI_THIRD_PARTY` that, when set to `OFF`, accelerates doxygen documentation generation or `user_version` for instance.
+
 ## Builds
 
 ### Linux
diff --git a/CMakeLists.txt b/CMakeLists.txt
index ac877eea..6c233459 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -13,8 +13,12 @@ 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 "src/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)
 
@@ -52,7 +56,9 @@ foreach(GUDHI_MODULE ${GUDHI_MODULES})
   endforeach()
 endforeach()
 
-add_subdirectory(src/GudhUI)
+if (WITH_GUDHI_THIRD_PARTY)
+  add_subdirectory(src/GudhUI)
+endif()
 
 if (WITH_GUDHI_PYTHON)
   # specific for cython module
diff --git a/ext/gudhi-deploy b/ext/gudhi-deploy
-Subproject 290ade1086bedbc96a35df886cadecabbf4072e
+Subproject e9e9a4878731853d2d3149a5eac30df338a8197
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/Doxyfile.in b/src/Doxyfile.in
index d0fad45f..fb68ceb1 100644
--- a/src/Doxyfile.in
+++ b/src/Doxyfile.in
@@ -711,7 +711,7 @@ 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 +765,7 @@ 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
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.