doc/doxygen/Doxyfile.handbook: update with new doxygen version

doc/doxygen/Doxyfile.handbook

@@ -1,4 +1,4 @@
-# Doxyfile 1.8.1.2
+# Doxyfile 1.8.3.1
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -88,7 +88,7 @@ BRIEF_MEMBER_DESC      = YES
 # Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
 # brief descriptions will be completely suppressed.
 
-REPEAT_BRIEF           = NO
+REPEAT_BRIEF           = YES
 
 # This tag implements a quasi-intelligent brief description abbreviator
 # that is used to form the text in various listings. Each string
@@ -126,7 +126,9 @@ FULL_PATH_NAMES        = YES
 # only done if one of the specified strings matches the left-hand part of
 # the path. The tag can be used to show relative paths in the file list.
 # If left blank the directory from which doxygen is run is used as the
-# path to strip.
+# path to strip. Note that you specify absolute paths here, but also
+# relative paths, which will be relative from the directory where doxygen is
+# started.
 
 STRIP_FROM_PATH        =
 
@@ -229,14 +231,15 @@ OPTIMIZE_FOR_FORTRAN   = NO
 OPTIMIZE_OUTPUT_VHDL   = NO
 
 # Doxygen selects the parser to use depending on the extension of the files it
-# parses. With this tag you can assign which parser to use for a given extension.
-# Doxygen has a built-in mapping, but you can override or extend it using this
-# tag. The format is ext=language, where ext is a file extension, and language
-# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C,
-# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make
-# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C
-# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions
-# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
+# parses. With this tag you can assign which parser to use for a given
+# extension. Doxygen has a built-in mapping, but you can override or extend it
+# using this tag. The format is ext=language, where ext is a file extension,
+# and language is one of the parsers supported by doxygen: IDL, Java,
+# Javascript, CSharp, C, C++, D, PHP, Objective-C, Python, Fortran, VHDL, C,
+# C++. For instance to make doxygen treat .inc files as Fortran files (default
+# is PHP), and .f files as C (default is Fortran), use: inc=Fortran f=C. Note
+# that for custom extensions you also need to set FILE_PATTERNS otherwise the
+# files are not read by doxygen.
 
 EXTENSION_MAPPING      =
 
@@ -249,6 +252,13 @@ EXTENSION_MAPPING      =
 
 MARKDOWN_SUPPORT       = YES
 
+# When enabled doxygen tries to link words that correspond to documented classes,
+# or namespaces to their corresponding documentation. Such a link can be
+# prevented in individual cases by by putting a % sign in front of the word or
+# globally by setting AUTOLINK_SUPPORT to NO.
+
+AUTOLINK_SUPPORT       = YES
+
 # If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
 # to include (a tag file for) the STL sources as input, then you should
 # set this tag to YES in order to let doxygen match functions declarations and
@@ -269,10 +279,10 @@ CPP_CLI_SUPPORT        = NO
 
 SIP_SUPPORT            = NO
 
-# For Microsoft's IDL there are propget and propput attributes to indicate getter
-# and setter methods for a property. Setting this option to YES (the default)
-# will make doxygen replace the get and set methods by a property in the
-# documentation. This will only work if the methods are indeed getting or
+# For Microsoft's IDL there are propget and propput attributes to indicate
+# getter and setter methods for a property. Setting this option to YES (the
+# default) will make doxygen replace the get and set methods by a property in
+# the documentation. This will only work if the methods are indeed getting or
 # setting a simple type. If this is not the case, or you want to show the
 # methods anyway, you should set this option to NO.
 
@@ -298,7 +308,7 @@ SUBGROUPING            = YES
 # @ingroup) instead of on a separate page (for HTML and Man pages) or
 # section (for LaTeX and RTF).
 
-INLINE_GROUPED_CLASSES = NO
+INLINE_GROUPED_CLASSES = YES
 
 # When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and
 # unions with only public data fields will be shown inline in the documentation
@@ -307,7 +317,7 @@ INLINE_GROUPED_CLASSES = NO
 # structs, classes, and unions are shown on a separate page (for HTML and Man
 # pages) or section (for LaTeX and RTF).
 
-INLINE_SIMPLE_STRUCTS  = NO
+INLINE_SIMPLE_STRUCTS  = YES
 
 # When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
 # is documented as struct, union, or enum with the name of the typedef. So
@@ -362,14 +372,15 @@ EXTRACT_ALL            = NO
 
 EXTRACT_PRIVATE        = YES
 
-# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal scope will be included in the documentation.
+# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal
+# scope will be included in the documentation.
 
 EXTRACT_PACKAGE        = NO
 
 # If the EXTRACT_STATIC tag is set to YES all static members of a file
 # will be included in the documentation.
 
-EXTRACT_STATIC         = NO
+EXTRACT_STATIC         = YES
 
 # If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
 # defined locally in source files will be included in the documentation.
@@ -533,7 +544,8 @@ GENERATE_BUGLIST       = YES
 GENERATE_DEPRECATEDLIST= YES
 
 # The ENABLED_SECTIONS tag can be used to enable conditional
-# documentation sections, marked by \if sectionname ... \endif.
+# documentation sections, marked by \if section-label ... \endif
+# and \cond section-label ... \endcond blocks.
 
 ENABLED_SECTIONS       =
 
@@ -591,7 +603,8 @@ LAYOUT_FILE            =
 # requires the bibtex tool to be installed. See also
 # http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style
 # of the bibliography can be controlled using LATEX_BIB_STYLE. To use this
-# feature you need bibtex and perl available in the search path.
+# feature you need bibtex and perl available in the search path. Do not use
+# file names with spaces, bibtex cannot handle them.
 
 CITE_BIB_FILES         =
 
@@ -655,26 +668,38 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  =  handbook/chapters/introduction.doxy \
-		       	  handbook/chapters/building.doxy \
-			  handbook/chapters/basic_examples.doxy \
-			  handbook/chapters/advanced_examples.doxy \
-			  handbook/chapters/optimize_performance.doxy \
-			  handbook/chapters/performance_feedback.doxy \
-			  handbook/chapters/tips_and_tricks.doxy \
-			  handbook/chapters/mpi_support.doxy \
-  			  handbook/chapters/fft_support.doxy \
-			  handbook/chapters/c_extensions.doxy \
-			  handbook/chapters/socl_opencl_extensions.doxy \
-			  handbook/chapters/scheduling_contexts.doxy \
-			  handbook/chapters/scheduling_context_hypervisor.doxy \
-			  handbook/chapters/api/initialization.doxy \
-			  handbook/chapters/api/versioning.doxy \
-			  handbook/chapters/api/standard_memory_library.doxy \
-			  ../../build/include/starpu_config.h \
-			  ../../include/starpu.h \
-			  ../../include/starpu_driver.h \
-			  ../../include/starpu_stdlib.h
+INPUT                  = chapters/introduction.doxy \
+                         chapters/building.doxy \
+                         chapters/basic_examples.doxy \
+                         chapters/advanced_examples.doxy \
+                         chapters/optimize_performance.doxy \
+                         chapters/performance_feedback.doxy \
+                         chapters/tips_and_tricks.doxy \
+                         chapters/mpi_support.doxy \
+                         chapters/fft_support.doxy \
+                         chapters/c_extensions.doxy \
+                         chapters/socl_opencl_extensions.doxy \
+                         chapters/scheduling_contexts.doxy \
+                         chapters/scheduling_context_hypervisor.doxy \
+                         chapters/api/initialization.doxy \
+                         chapters/api/versioning.doxy \
+                         chapters/api/standard_memory_library.doxy \
+                         chapters/api/workers.doxy \
+                         chapters/api/data_management.doxy \
+                         chapters/api/data_interfaces.doxy \
+                         chapters/api/data_partition.doxy \
+                         chapters/api/multiformat_data_interface.doxy \
+                         chapters/api/codelet_and_tasks.doxy \
+                         ../../build/include/starpu_config.h \
+                         ../../include/starpu.h \
+                         ../../include/starpu_driver.h \
+                         ../../include/starpu_stdlib.h \
+                         ../../include/starpu_worker.h \
+                         ../../include/starpu_data.h \
+                         ../../include/starpu_data_interfaces.h \
+                         ../../include/starpu_data_filters.h \
+                         ../../include/starpu_hash.h \
+                         ../../include/starpu_task.h
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
@@ -765,7 +790,7 @@ IMAGE_PATH             =
 # If FILTER_PATTERNS is specified, this tag will be
 # ignored.
 
-INPUT_FILTER           =
+INPUT_FILTER           = "sed 's,STARPU_DEPRECATED,,'"
 
 # The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
 # basis.
@@ -792,6 +817,13 @@ FILTER_SOURCE_FILES    = NO
 
 FILTER_SOURCE_PATTERNS =
 
+# If the USE_MD_FILE_AS_MAINPAGE tag refers to the name of a markdown file that
+# is part of the input, its contents will be placed on the main page (index.html).
+# This can be useful if you have a project on for instance GitHub and want reuse
+# the introduction page also for the doxygen output.
+
+USE_MDFILE_AS_MAINPAGE =
+
 #---------------------------------------------------------------------------
 # configuration options related to source browsing
 #---------------------------------------------------------------------------
@@ -913,13 +945,23 @@ HTML_FOOTER            =
 
 # The HTML_STYLESHEET tag can be used to specify a user-defined cascading
 # style sheet that is used by each HTML page. It can be used to
-# fine-tune the look of the HTML output. If the tag is left blank doxygen
-# will generate a default style sheet. Note that doxygen will try to copy
-# the style sheet file to the HTML output directory, so don't put your own
-# style sheet in the HTML output directory as well, or it will be erased!
+# fine-tune the look of the HTML output. If left blank doxygen will
+# generate a default style sheet. Note that it is recommended to use
+# HTML_EXTRA_STYLESHEET instead of this one, as it is more robust and this
+# tag will in the future become obsolete.
 
 HTML_STYLESHEET        =
 
+# The HTML_EXTRA_STYLESHEET tag can be used to specify an additional
+# user-defined cascading style sheet that is included after the standard
+# style sheets created by doxygen. Using this option one can overrule
+# certain style aspects. This is preferred over using HTML_STYLESHEET
+# since it does not replace the standard style sheet and is therefor more
+# robust against future updates. Doxygen will copy the style sheet file to
+# the output directory.
+
+HTML_EXTRA_STYLESHEET  =
+
 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
 # other source files which should be copied to the HTML output directory. Note
 # that these files will be copied to the base HTML output directory. Use the
@@ -1004,9 +1046,9 @@ DOCSET_FEEDNAME        = "Doxygen generated docs"
 
 DOCSET_BUNDLE_ID       = org.doxygen.Project
 
-# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
-# the documentation publisher. This should be a reverse domain-name style
-# string, e.g. com.mycompany.MyDocSet.documentation.
+# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely
+# identify the documentation publisher. This should be a reverse domain-name
+# style string, e.g. com.mycompany.MyDocSet.documentation.
 
 DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
 
@@ -1191,6 +1233,13 @@ FORMULA_TRANSPARENT    = YES
 
 USE_MATHJAX            = NO
 
+# When MathJax is enabled you can set the default output format to be used for
+# thA MathJax output. Supported types are HTML-CSS, NativeMML (i.e. MathML) and
+# SVG. The default value is HTML-CSS, which is slower, but has the best
+# compatibility.
+
+MATHJAX_FORMAT         = HTML-CSS
+
 # When MathJax is enabled you need to specify the location relative to the
 # HTML output directory using the MATHJAX_RELPATH option. The destination
 # directory should contain the MathJax.js script. For instance, if the mathjax
@@ -1219,15 +1268,55 @@ MATHJAX_EXTENSIONS     =
 SEARCHENGINE           = YES
 
 # When the SERVER_BASED_SEARCH tag is enabled the search engine will be
-# implemented using a PHP enabled web server instead of at the web client
-# using Javascript. Doxygen will generate the search PHP script and index
-# file to put on the web server. The advantage of the server
-# based approach is that it scales better to large projects and allows
-# full text search. The disadvantages are that it is more difficult to setup
-# and does not have live searching capabilities.
+# implemented using a web server instead of a web client using Javascript.
+# There are two flavours of web server based search depending on the
+# EXTERNAL_SEARCH setting. When disabled, doxygen will generate a PHP script for
+# searching and an index file used by the script. When EXTERNAL_SEARCH is
+# enabled the indexing and searching needs to be provided by external tools.
+# See the manual for details.
 
 SERVER_BASED_SEARCH    = NO
 
+# When EXTERNAL_SEARCH is enabled doxygen will no longer generate the PHP
+# script for searching. Instead the search results are written to an XML file
+# which needs to be processed by an external indexer. Doxygen will invoke an
+# external search engine pointed to by the SEARCHENGINE_URL option to obtain
+# the search results. Doxygen ships with an example indexer (doxyindexer) and
+# search engine (doxysearch.cgi) which are based on the open source search engine
+# library Xapian. See the manual for configuration details.
+
+EXTERNAL_SEARCH        = NO
+
+# The SEARCHENGINE_URL should point to a search engine hosted by a web server
+# which will returned the search results when EXTERNAL_SEARCH is enabled.
+# Doxygen ships with an example search engine (doxysearch) which is based on
+# the open source search engine library Xapian. See the manual for configuration
+# details.
+
+SEARCHENGINE_URL       =
+
+# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
+# search data is written to a file for indexing by an external tool. With the
+# SEARCHDATA_FILE tag the name of this file can be specified.
+
+SEARCHDATA_FILE        = searchdata.xml
+
+# When SERVER_BASED_SEARCH AND EXTERNAL_SEARCH are both enabled the
+# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
+# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
+# projects and redirect the results back to the right project.
+
+EXTERNAL_SEARCH_ID     =
+
+# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
+# projects other than the one defined by this configuration file, but that are
+# all added to the same external search index. Each project needs to have a
+# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id
+# of to a relative location where the documentation can be found.
+# The format is: EXTRA_SEARCH_MAPPINGS = id1=loc1 id2=loc2 ...
+
+EXTRA_SEARCH_MAPPINGS  =
+
 #---------------------------------------------------------------------------
 # configuration options related to the LaTeX output
 #---------------------------------------------------------------------------
@@ -1279,7 +1368,7 @@ EXTRA_PACKAGES         =
 # the first chapter. If it is left blank doxygen will generate a
 # standard header. Notice: only use this tag if you know what you are doing!
 
-#LATEX_HEADER           =   handbook/chapters/refman.tex
+#LATEX_HEADER           = chapters/refman.tex
 
 # The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for
 # the generated latex document. The footer should contain everything after
@@ -1528,7 +1617,9 @@ INCLUDE_FILE_PATTERNS  =
 # undefined via #undef or recursively expanded use the := operator
 # instead of the = operator.
 
-PREDEFINED             = STARPU_USE_OPENCL=1
+PREDEFINED             = STARPU_USE_OPENCL=1 \
+                         STARPU_USE_CUDA=1 \
+                         __GCC__
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
 # this tag can be used to specify a list of macro names that should be expanded.