Merge pull request #156 from VincentRouvreau/gudhi_citation_update

Fix #101
Fix #102

5 files changed, 17 insertions, 11 deletions

diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h
index adc1378f..3c32a1e6 100644
--- a/src/Alpha_complex/doc/Intro_alpha_complex.h
+++ b/src/Alpha_complex/doc/Intro_alpha_complex.h
@@ -38,12 +38,12 @@ namespace alpha_complex {
  *
  * Alpha_complex is constructing a <a target="_blank"
  * href="http://doc.cgal.org/latest/Triangulation/index.html#Chapter_Triangulations">Delaunay Triangulation</a>
- * \cite cgal:hdj-t-15b from <a target="_blank" href="http://www.cgal.org/">CGAL</a> (the Computational Geometry
- * Algorithms Library \cite cgal:eb-15b) and is able to create a `SimplicialComplexForAlpha`.
+ * \cite cgal:hdj-t-19b from <a target="_blank" href="http://www.cgal.org/">CGAL</a> (the Computational Geometry
+ * Algorithms Library \cite cgal:eb-19b) and is able to create a `SimplicialComplexForAlpha`.
  *
  * The complex is a template class requiring an Epick_d <a target="_blank"
  * href="http://doc.cgal.org/latest/Kernel_d/index.html#Chapter_dD_Geometry_Kernel">dD Geometry Kernel</a>
- * \cite cgal:s-gkd-15b from CGAL as template parameter.
+ * \cite cgal:s-gkd-19b from CGAL as template parameter.
  *
  * \remark
  * - When the simplicial complex is constructed with an infinite value of alpha, the complex is a Delaunay
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h
index 0c2569c8..6b4d8463 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h
@@ -72,7 +72,7 @@ template<typename D> struct Is_Epeck_D<CGAL::Epeck_d<D>> { static const bool val
  * or an <a target="_blank"
  * href="https://doc.cgal.org/latest/Kernel_d/structCGAL_1_1Epick__d.html">CGAL::Epick_d</a> <a target="_blank"
  * href="http://doc.cgal.org/latest/Kernel_d/index.html#Chapter_dD_Geometry_Kernel">dD Geometry Kernel</a>
- * \cite cgal:s-gkd-15b from CGAL as template, default value is <a target="_blank"
+ * \cite cgal:s-gkd-19b from CGAL as template, default value is <a target="_blank"
  * href="https://doc.cgal.org/latest/Kernel_d/structCGAL_1_1Epeck__d.html">CGAL::Epeck_d</a>
  * < <a target="_blank" href="http://doc.cgal.org/latest/Kernel_23/classCGAL_1_1Dynamic__dimension__tag.html">
  * CGAL::Dynamic_dimension_tag </a> >
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)
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
index 2e64bef8..c320e7e0 100644
--- a/src/common/doc/installation.h
+++ b/src/common/doc/installation.h
@@ -71,7 +71,7 @@ make doxygen
  * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html
  * 
  * The following examples/utilities require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms
- * Library</a> (CGAL \cite cgal:eb-15b) and will not be built if CGAL version 4.11.0 or higher is not installed:
+ * Library</a> (CGAL \cite cgal:eb-19b) and will not be built if CGAL version 4.11.0 or higher is not installed:
  * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
  * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a>
  * \li <a href="_witness_complex_2strong_witness_persistence_8cpp-example.html">
diff --git a/src/python/doc/alpha_complex_user.rst b/src/python/doc/alpha_complex_user.rst
index 950db3cd..b7e69e12 100644
--- a/src/python/doc/alpha_complex_user.rst
+++ b/src/python/doc/alpha_complex_user.rst
@@ -11,8 +11,8 @@ Definition
 
 `AlphaComplex` is constructing a :doc:`SimplexTree <simplex_tree_ref>` using
 `Delaunay Triangulation  <http://doc.cgal.org/latest/Triangulation/index.html#Chapter_Triangulations>`_ 
-:cite:`cgal:hdj-t-15b` from `CGAL <http://www.cgal.org/>`_ (the Computational Geometry Algorithms Library
-:cite:`cgal:eb-15b`).
+:cite:`cgal:hdj-t-19b` from `CGAL <http://www.cgal.org/>`_ (the Computational Geometry Algorithms Library
+:cite:`cgal:eb-19b`).
 
 Remarks
 ^^^^^^^