Merge remote-tracking branch 'origin/master' into OSCAR

CMakeLists.txt

@@ -327,6 +327,10 @@ if (HEPMC3_INSTALL_EXAMPLES)
   install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/examples/ DESTINATION  ${CMAKE_INSTALL_DOCDIR}/examples COMPONENT doc
           FILES_MATCHING PATTERN "*"
           PATTERN "*CMakeFiles*" EXCLUDE
+          PATTERN "*myclass_Classes.cxx" EXCLUDE
+          PATTERN "*pcm" EXCLUDE
+          PATTERN "*rootmap" EXCLUDE
+          PATTERN "*Dict.cxx" EXCLUDE
           PATTERN "Makefile" EXCLUDE
           PATTERN "*cmake_install.cmake*" EXCLUDE
           PATTERN "*libAnalysis*" EXCLUDE )

doc/doxygen/Doxyfile.in

@@ -974,12 +974,6 @@ HTML_COLORSTYLE_SAT    = 100
 
 HTML_COLORSTYLE_GAMMA  = 80
 
-# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
-# page will contain the date and time when the page was generated. Setting
-# this to NO can help when comparing the output of multiple runs.
-
-HTML_TIMESTAMP         = YES
-
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded.
@@ -1194,14 +1188,6 @@ EXT_LINKS_IN_WINDOW    = NO
 
 FORMULA_FONTSIZE       = 10
 
-# Use the FORMULA_TRANPARENT tag to determine whether or not the images
-# generated for formulas are transparent PNGs. Transparent PNGs are
-# not supported properly for IE 6.0, but are supported on all modern browsers.
-# Note that when changing this option you need to delete any form_*.png files
-# in the HTML output before the changes have effect.
-
-FORMULA_TRANSPARENT    = YES
-
 # Enable the USE_MATHJAX option to render LaTeX formulas using MathJax
 # (see http://www.mathjax.org) which uses client side Javascript for the
 # rendering instead of using prerendered bitmaps. Use this if you do not
@@ -1381,13 +1367,6 @@ LATEX_BATCHMODE        = NO
 
 LATEX_HIDE_INDICES     = NO
 
-# If LATEX_SOURCE_CODE is set to YES then doxygen will include
-# source code with syntax highlighting in the LaTeX output.
-# Note that which sources are shown also depends on other settings
-# such as SOURCE_BROWSER.
-
-LATEX_SOURCE_CODE      = NO
-
 # The LATEX_BIB_STYLE tag can be used to specify the style to use for the
 # bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See
 # http://en.wikipedia.org/wiki/BibTeX for more info.
@@ -1657,14 +1636,6 @@ EXTERNAL_GROUPS        = YES
 # Configuration options related to the dot tool
 #---------------------------------------------------------------------------
 
-# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
-# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
-# or super classes. Setting the tag to NO turns the diagrams off. Note that
-# this option also works with HAVE_DOT disabled, but it is recommended to
-# install and use dot, since it yields more powerful graphs.
-
-CLASS_DIAGRAMS         = YES
-
 # You can define message sequence charts within doxygen comments using the \msc
 # command. Doxygen will then run the mscgen tool (see
 # http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
@@ -1695,20 +1666,6 @@ HAVE_DOT               = YES
 
 DOT_NUM_THREADS        = 0
 
-# By default doxygen will use the Helvetica font for all dot files that
-# doxygen generates. When you want a differently looking font you can specify
-# the font name using DOT_FONTNAME. You need to make sure dot is able to find
-# the font, which can be done by putting it in a standard location or by setting
-# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the
-# directory containing the font.
-
-DOT_FONTNAME           = Helvetica
-
-# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
-# The default size is 10pt.
-
-DOT_FONTSIZE           = 10
-
 # By default doxygen will tell dot to use the Helvetica font.
 # If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to
 # set the path where dot can find it.
@@ -1850,14 +1807,6 @@ DOT_GRAPH_MAX_NODES    = 150
 
 MAX_DOT_GRAPH_DEPTH    = 0
 
-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, because dot on Windows does not
-# seem to support this out of the box. Warning: Depending on the platform used,
-# enabling this option may lead to badly anti-aliased labels on the edges of
-# a graph (i.e. they become hard to read).
-
-DOT_TRANSPARENT        = NO
-
 # Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
 # files in one run (i.e. multiple -o and -T options on the command line). This
 # makes dot run faster, but since only newer versions of dot (>1.8.10)

doc/doxygen/differences.txt

@@ -303,7 +303,7 @@
         // Replace with:
         HepMC3::FourVector position(pos[1],pos[2],pos[3],pos[0]);
         HepMC3::GenVertexPtr vertex = std::make_shared<HepMC3::GenVertex>(position);
-        vertex->set_id(1);
+        vertex->set_status(1);
     @endcode
 
     @code{.cpp}

examples/ConvertExample/CMakeLists.txt

@@ -87,7 +87,6 @@ configure_file(
 if (USE_INSTALLED_HEPMC3)
   install(TARGETS convert_example.exe DESTINATION ${CMAKE_INSTALL_BINDIR})
   install(TARGETS Analysis DESTINATION ${CMAKE_INSTALL_BINDIR})
-  install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} DESTINATION ${CMAKE_INSTALL_BINDIR} FILES_MATCHING PATTERN "*.pcm" PATTERN "*config"  PATTERN "CMakeFiles" PATTERN  "*.ilk"  EXCLUDE)
   install(DIRECTORY ${PROJECT_BINARY_DIR}/outputs/${CMAKE_INSTALL_BINDIR}/ DESTINATION ${CMAKE_INSTALL_BINDIR}  FILES_MATCHING PATTERN "*env.sh*" )
 endif()
 

examples/RootIOExample2/CMakeLists.txt

@@ -40,8 +40,7 @@ configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/class_example_env.sh.in
 # installs
 if (USE_INSTALLED_HEPMC3)
   install(TARGETS class_example_write.exe class_example_read.exe DESTINATION ${CMAKE_INSTALL_BINDIR})
-  install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} DESTINATION ${CMAKE_INSTALL_BINDIR} FILES_MATCHING PATTERN "*.pcm" PATTERN "*config" PATTERN "CMakeFiles" EXCLUDE )
-  install(FILES example.hepmc3 DESTINATION ${CMAKE_INSTALL_BINDIR})
+  install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/example.hepmc3 ${CMAKE_CURRENT_BINARY_DIR}/libmyclass_Classes_rdict.pcm  ${CMAKE_CURRENT_BINARY_DIR}/libmyclass_Classes.rootmap  DESTINATION ${CMAKE_INSTALL_BINDIR})
   install(DIRECTORY ${PROJECT_BINARY_DIR}/outputs/${CMAKE_INSTALL_BINDIR}/ DESTINATION ${CMAKE_INSTALL_BINDIR}
         FILES_MATCHING PATTERN "*env.sh*")
 endif()

examples/ViewerExample/CMakeLists.txt

@@ -6,22 +6,16 @@ endforeach()
 find_package(Graphviz)
 find_package(ROOT REQUIRED COMPONENTS Core RIO Tree Gui Graf Hist Gpad )
 if(Graphviz_FOUND AND ROOT_FOUND)
-  message(STATUS "HepMC3 ViewerExample: GrpahViz and ROOT found. GUI Browser example enabled. ${ROOT_LIBRARIES}  ${Graphviz_GRAPH_LIBRARY}  ${Graphviz_CGRAPH_LIBRARY} ${Graphviz_GVC_LIBRARY} ${Graphviz_INCLUDE_DIRS}")
-  include_directories(${PROJECT_SOURCE_DIR}/rootIO/include ${CMAKE_CURRENT_SOURCE_DIR}/include ${CMAKE_CURRENT_SOURCE_DIR}  ${ROOT_INCLUDE_DIRS} ${Graphviz_INCLUDE_DIRS} ./)
+  message(STATUS "HepMC3 ViewerExample: GraphViz and ROOT found. GUI Browser example enabled. ${ROOT_LIBRARIES}  ${Graphviz_GRAPH_LIBRARY}  ${Graphviz_CGRAPH_LIBRARY} ${Graphviz_GVC_LIBRARY} ${Graphviz_INCLUDE_DIRS}")
+  include_directories(${PROJECT_SOURCE_DIR}/rootIO/include ${CMAKE_CURRENT_SOURCE_DIR}/include ${CMAKE_CURRENT_SOURCE_DIR} ./)
   ROOT_GENERATE_DICTIONARY(HepMC3ViewerFrameDict include/HepMC3ViewerFrame.h LINKDEF include/LinkDef.h OPTIONS -inlineInputHeader)
   ADD_EXECUTABLE(HepMC3Viewer.exe  src/main.cc  src/HepMC3ViewerFrame.cc HepMC3ViewerFrameDict.cxx  )
   set_target_properties(HepMC3Viewer.exe PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/outputs/${CMAKE_INSTALL_BINDIR})
-  target_compile_definitions(HepMC3Viewer.exe PRIVATE ${Graphviz_DEFINES} )
   include_directories( include  )
-
-  SET(linklibraties   ${Graphviz_CGRAPH_LIBRARY}  ${Graphviz_GVC_LIBRARY}  HepMC3::HepMC3 HepMC3::rootIO )
-  if (Graphviz_GRAPH_LIBRARY)
-    list(APPEND linklibraties  ${Graphviz_GRAPH_LIBRARY}  )
-  endif()
-  TARGET_LINK_LIBRARIES(HepMC3Viewer.exe   ${linklibraties} ROOT::Core ROOT::RIO ROOT::Tree  ROOT::Gui ROOT::Graf ROOT::Hist ROOT::Gpad)
+  TARGET_LINK_LIBRARIES(HepMC3Viewer.exe   Graphviz::CGRAPH Graphviz::GVC HepMC3::HepMC3 HepMC3::rootIO  ROOT::Core ROOT::RIO ROOT::Tree  ROOT::Gui ROOT::Graf ROOT::Hist ROOT::Gpad)
   if (USE_INSTALLED_HEPMC3)
     install(TARGETS HepMC3Viewer.exe DESTINATION ${CMAKE_INSTALL_BINDIR})
-    install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} DESTINATION ${CMAKE_INSTALL_BINDIR} FILES_MATCHING PATTERN "*.pcm" PATTERN "*config"  PATTERN "CMakeFiles" EXCLUDE )
+    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libHepMC3ViewerFrameDict_rdict.pcm  ${CMAKE_CURRENT_BINARY_DIR}/libHepMC3ViewerFrameDict.rootmap DESTINATION ${CMAKE_INSTALL_BINDIR})
     install(DIRECTORY ${PROJECT_BINARY_DIR}/outputs/${CMAKE_INSTALL_BINDIR}/ DESTINATION ${CMAKE_INSTALL_BINDIR}
         FILES_MATCHING PATTERN "*env.sh*")
   endif()

examples/ViewerExample/cmake/Modules/FindGraphviz.cmake

@@ -7,19 +7,19 @@
 #  Graphviz_INCLUDE_DIRS (not cached)
 #  Graphviz_CGRAPH_LIBRARY
 #  Graphviz_GVC_LIBRARY
-if (Graphviz_DIR OR Graphviz_DIR OR (DEFINED ENV{Graphviz_DIR}) OR (DEFINED ENV{Graphviz_DIR}) )
+if (Graphviz_DIR OR GRAPHVIZ_DIR OR (DEFINED ENV{Graphviz_DIR}) OR (DEFINED ENV{GRAPHVIZ_DIR}) )
   set(Graphviz_SEARCH_DIRS "" CACHE STRING "" FORCE)
   if (Graphviz_DIR)
     list (APPEND Graphviz_SEARCH_DIRS "${Graphviz_DIR}" )
   endif()
-  if (Graphviz_DIR)
-    list (APPEND Graphviz_SEARCH_DIRS "${Graphviz_DIR}" )
+  if (GRAPHVIZ_DIR)
+    list (APPEND Graphviz_SEARCH_DIRS "${GRAPHVIZ_DIR}" )
   endif()
   if (DEFINED ENV{Graphviz_DIR})
     list (APPEND Graphviz_SEARCH_DIRS "$ENV{Graphviz_DIR}" )
   endif()
-  if (DEFINED ENV{Graphviz_DIR})
-    list (APPEND Graphviz_SEARCH_DIRS "ENV{Graphviz_DIR}" )
+  if (DEFINED ENV{GRAPHVIZ_DIR})
+    list (APPEND Graphviz_SEARCH_DIRS "ENV{GRAPHVIZ_DIR}" )
   endif()
 endif()
 
@@ -36,16 +36,37 @@ endif()
 set(Graphviz_INCLUDE_DIRS ${Graphviz_INCLUDE_DIR} ${Graphviz_INCLUDE_DIR}/graphviz)
 get_filename_component(Graphviz_LIBRARY_DIR ${Graphviz_GVC_LIBRARY} PATH)
 set ( TEST_SOURCE "#include <graphviz/gvc.h>\n#include <string>\n #include <graphviz/cdt.h>\n int main(){\nreturn strcmp(\"XX\",\"XXY\");\n}\n")
+if (Graphviz_INCLUDE_DIR)
+  set(CMAKE_REQUIRED_INCLUDES ${Graphviz_INCLUDE_DIRS})
+endif()
 check_cxx_source_compiles("${TEST_SOURCE}" TEST_SOURCE_NOAST_COMPILES )
 check_cxx_source_compiles("#define _PACKAGE_ast 1\n${TEST_SOURCE}" TEST_SOURCE_AST_COMPILES )
 if (TEST_SOURCE_AST_COMPILES AND (NOT TEST_SOURCE_NOAST_COMPILES))
-  set(Graphviz_DEFINES "-D_PACKAGE_ast=1")
+  set(Graphviz_DEFINES "_PACKAGE_ast=1")
 else()
-  set(Graphviz_DEFINES "-D_UNUSED_DUMMY_DEFINE")  
+  set(Graphviz_DEFINES "_UNUSED_DUMMY_DEFINE")  
 endif()
 
 INCLUDE(FindPackageHandleStandardArgs)
 
 FIND_PACKAGE_HANDLE_STANDARD_ARGS(Graphviz FOUND_VAR Graphviz_FOUND REQUIRED_VARS Graphviz_DEFINES Graphviz_INCLUDE_DIR Graphviz_CGRAPH_LIBRARY Graphviz_GVC_LIBRARY  HANDLE_COMPONENTS)
 
+
+if(Graphviz_FOUND AND NOT TARGET Graphviz::CGRAPH)
+    add_library(Graphviz::CGRAPH UNKNOWN IMPORTED)
+    set_target_properties(Graphviz::CGRAPH PROPERTIES
+        IMPORTED_LOCATION "${Graphviz_CGRAPH_LIBRARY}"
+        INTERFACE_INCLUDE_DIRECTORIES "${Graphviz_INCLUDE_DIRS}"
+        INTERFACE_COMPILE_DEFINITIONS "${Graphviz_DEFINES}"        
+    )
+endif()
+if(Graphviz_FOUND AND NOT TARGET Graphviz::GVC)
+    add_library(Graphviz::GVC UNKNOWN IMPORTED)
+    set_target_properties(Graphviz::GVC PROPERTIES
+        IMPORTED_LOCATION "${Graphviz_GVC_LIBRARY}"
+        INTERFACE_INCLUDE_DIRECTORIES "${Graphviz_INCLUDE_DIRS}"
+        INTERFACE_COMPILE_DEFINITIONS "${Graphviz_DEFINES}"
+    )
+endif()
+
 mark_as_advanced(Graphviz_FOUND Graphviz_INCLUDE_DIRS Graphviz_CGRAPH_LIBRARY Graphviz_GVC_LIBRARY Graphviz_DEFINES)

include/HepMC3/GenCrossSection.h

@@ -62,8 +62,14 @@ class GenCrossSection : public Attribute {
     bool to_string(std::string &att) const override;
     /// @name Deprecated functionality
     /// @{
-    /// @brief Set all fields
-    /// @deprecated Use set_cross_section(const std::vector<double>& xs, const std::vector<double>& xs_err instead
+    /** @brief Set all fields
+        @deprecated Use set_cross_section(const std::vector<double>& xs, const std::vector<double>& xs_err instead
+       
+        @param xs Cross section
+        @param xs_err Uncertainty on cross-section
+        @param n_acc Number of accepted events
+        @param n_att Number of attempted events
+    */
     void set_cross_section(const double& xs, const double& xs_err,const long& n_acc = -1, const long& n_att = -1);
 
     /// @}

include/HepMC3/GenEvent.h

@@ -80,13 +80,14 @@ class GenEvent {
 
     /// @name Particle and vertex access
     /// @{
-    /// Particles size, HepMC2 compatibility
+
+    /// @brief Particles size, HepMC2 compatibility
     inline int particles_size() const { return m_particles.size(); }
-    /// Particles empty, HepMC2 compatibility
+    /// @brief Particles empty, HepMC2 compatibility
     inline bool particles_empty() const { return m_particles.empty(); }
-    /// Vertices size, HepMC2 compatibility
+    /// @brief Vertices size, HepMC2 compatibility
     inline int vertices_size() const { return m_vertices.size(); }
-    /// Vertices empty, HepMC2 compatibility
+    /// @brief Vertices empty, HepMC2 compatibility
     inline bool vertices_empty() const { return m_vertices.empty(); }
     /// @}
 

include/HepMC3/GenVertex.h

@@ -38,7 +38,6 @@ class GenVertex : public std::enable_shared_from_this<GenVertex> {
 
     /// @}
 
-public:
 
     /// @name Accessors
     /// @{
@@ -57,9 +56,6 @@ class GenVertex : public std::enable_shared_from_this<GenVertex> {
     /// @note This is not the same as id() in HepMC v2, which is now @c status()
     int id() const { return m_id; }
 
-    /// @brief set the vertex identifier
-    void set_id(int id);
-
     /// Get vertex status code
     int status() const { return m_data.status; }
     /// Set vertex status code

include/HepMC3/ReaderAscii.h

@@ -19,8 +19,10 @@
 #include <fstream>
 #include <istream>
 #include <iterator>
+#include <unordered_map>
 #include "HepMC3/Reader.h"
 #include "HepMC3/GenEvent.h"
+#include "HepMC3/Data/GenEventData.h"
 
 
 namespace HepMC3 {
@@ -67,69 +69,61 @@ class ReaderAscii : public Reader {
     /// @brief Parse event
     ///
     /// Helper routine for parsing event information
-    /// @param[out] evt Event that will be filled with new data
     /// @param[in]  buf Line of text that needs to be parsed
     /// @return vertices count and particles count for verification
-    std::pair<int,int> parse_event_information(GenEvent &evt, const char *buf);
+    std::pair<int,int> parse_event_information(const char *buf);
 
     /// @brief Parse weight value lines
     ///
     /// Helper routine for parsing weight value information
-    /// @param[out] evt Event whose GenWeights will be filled with weight values
     /// @param[in]  buf Line of text that needs to be parsed
     ///
-    bool parse_weight_values(GenEvent &evt, const char *buf);
+    bool parse_weight_values(const char *buf);
 
     /// @brief Parse units
     ///
     /// Helper routine for parsing units information
-    /// @param[out] evt Event that will be filled with unit information
     /// @param[in]  buf Line of text that needs to be parsed
     ///
-    bool parse_units(GenEvent &evt, const char *buf);
+    bool parse_units(const char *buf);
 
     /// @brief Parse struct GenPdfInfo information
     ///
     /// Helper routine for parsing PDF information
-    /// @param[out] evt Event that will be filled with unit information
     /// @param[in]  buf Line of text that needs to be parsed
-    bool parse_pdf_info(GenEvent &evt, const char *buf);
+    bool parse_pdf_info(const char *buf);
 
     /// @brief Parse struct GenHeavyIon information
     ///
     /// Helper routine for parsing heavy ion information
-    /// @param[out] evt Event that will be filled with unit information
     /// @param[in]  buf Line of text that needs to be parsed
-    bool parse_heavy_ion(GenEvent &evt, const char *buf);
+    bool parse_heavy_ion(const char *buf);
 
     /// @brief Parse struct GenCrossSection information
     ///
     /// Helper routine for parsing cross-section information
-    /// @param[out] evt Event that will be filled with unit information
     /// @param[in]  buf Line of text that needs to be parsed
-    bool parse_cross_section(GenEvent &evt, const char *buf);
+    bool parse_cross_section( const char *buf);
 
     /// @brief Parse vertex
     ///
     /// Helper routine for parsing single event information
-    /// @param[out] evt Event that will contain parsed vertex
     /// @param[in] buf Line of text that needs to be parsed
     ///
-    bool parse_vertex_information(GenEvent &evt, const char *buf);
+    bool parse_vertex_information(const char *buf);
 
     /// @brief Parse particle
     ///
     /// Helper routine for parsing single particle information
     /// @param[out] evt Event that will contain parsed particle
     /// @param[in] buf Line of text that needs to be parsed
-    bool parse_particle_information(GenEvent &evt, const char *buf);
+    bool parse_particle_information(const char *buf);
 
     /// @brief Parse attribute
     ///
     /// Helper routine for parsing single attribute information
-    /// @param[out] evt Event that will contain parsed attribute
     /// @param[in] buf Line of text that needs to be parsed
-    bool parse_attribute(GenEvent &evt, const char *buf);
+    bool parse_attribute( const char *buf);
 
     /// @brief Parse run-level attribute.
     ///
@@ -160,15 +154,16 @@ class ReaderAscii : public Reader {
     std::istream* m_stream; ///< For ctor when reading from stream
     bool m_isstream; ///< toggles usage of m_file or m_stream
 
-
-    /** @brief Store attributes global to the run being written/read. */
-    std::map< std::string, std::shared_ptr<Attribute> > m_global_attributes;
-
-    /** @brief Temp storage for  outgoing particle ids */
-    std::map<GenVertexPtr, std::set<int> >  m_forward_mothers;
-    /** @brief Temp storage for  prod vertex ids */
-    std::map<GenParticlePtr, int >  m_forward_daughters;
-
+    /** @brief Temp storage for sets of incoming/outgoing ids for explicit vertices.*/
+    std::map<int, std::pair< std::set<int>, std::set<int> > >  m_io_explicit;
+    /** @brief Temp storage for sets of incoming/outgoing ids for implicit vertices.*/
+    std::unordered_map<int, std::pair< std::set<int>, std::set<int> > >  m_io_implicit;
+    /** @brief Temp storage to keep the order of implicit vertices.*/
+    std::vector<int> m_io_implicit_ids;
+    /** @brief Temp storage to keep the order of explicit vertices.*/
+    std::set<int> m_io_explicit_ids;
+
+    GenEventData m_data;
 };