diff options
Diffstat (limited to 'src/Doxyfile.in')
| -rw-r--r-- | src/Doxyfile.in | 585 |
1 files changed, 336 insertions, 249 deletions
diff --git a/src/Doxyfile.in b/src/Doxyfile.in index 57775498..d5664a49 100644 --- a/src/Doxyfile.in +++ b/src/Doxyfile.in @@ -1,4 +1,4 @@ -# Doxyfile 1.8.6 +# Doxyfile 1.8.13 # This file describes the settings to be used by the documentation system # doxygen (www.doxygen.org) for a project. @@ -32,7 +32,7 @@ DOXYFILE_ENCODING = UTF-8 # title of most generated pages and in a few other places. # The default value is: My Project. -PROJECT_NAME = "GUDHI" +PROJECT_NAME = "@CMAKE_PROJECT_NAME@" # The PROJECT_NUMBER tag can be used to enter a project or revision number. This # could be handy for archiving the generated documentation or if some version @@ -46,10 +46,10 @@ PROJECT_NUMBER = "@GUDHI_VERSION@" PROJECT_BRIEF = "C++ library for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding." -# With the PROJECT_LOGO tag one can specify an logo or icon that is included in -# the documentation. The maximum height of the logo should not exceed 55 pixels -# and the maximum width should not exceed 200 pixels. Doxygen will copy the logo -# to the output directory. +# With the PROJECT_LOGO tag one can specify a logo or an icon that is included +# in the documentation. The maximum height of the logo should not exceed 55 +# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy +# the logo to the output directory. PROJECT_LOGO = @@ -58,9 +58,9 @@ PROJECT_LOGO = # entered, it will be relative to the location where doxygen was started. If # left blank the current directory will be used. -OUTPUT_DIRECTORY = "doc/" +OUTPUT_DIRECTORY = -# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 4096 sub- +# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub- # directories (in 2 levels) under the output directory of each output format and # will distribute the generated files over these directories. Enabling this # option can be useful when feeding doxygen a huge amount of source files, where @@ -70,6 +70,14 @@ OUTPUT_DIRECTORY = "doc/" CREATE_SUBDIRS = NO +# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII +# characters to appear in the names of generated files. If set to NO, non-ASCII +# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode +# U+3044. +# The default value is: NO. + +ALLOW_UNICODE_NAMES = NO + # The OUTPUT_LANGUAGE tag is used to specify the language in which all # documentation generated by doxygen is written. Doxygen will use this # information to generate all constant output in the proper language. @@ -85,14 +93,14 @@ CREATE_SUBDIRS = NO OUTPUT_LANGUAGE = English -# If the BRIEF_MEMBER_DESC tag is set to YES doxygen will include brief member +# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member # descriptions after the members that are listed in the file and class # documentation (similar to Javadoc). Set to NO to disable this. # The default value is: YES. BRIEF_MEMBER_DESC = YES -# If the REPEAT_BRIEF tag is set to YES doxygen will prepend the brief +# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief # description of a member or function before the detailed description # # Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the @@ -127,7 +135,7 @@ ALWAYS_DETAILED_SEC = NO INLINE_INHERITED_MEMB = NO -# If the FULL_PATH_NAMES tag is set to YES doxygen will prepend the full path +# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path # before files name in the file list and in the header files. If set to NO the # shortest path that makes the file name unique will be used # The default value is: YES. @@ -144,7 +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 @@ -153,7 +161,9 @@ STRIP_FROM_PATH = # specify the list of include paths that are normally passed to the compiler # using the -I flag. -STRIP_FROM_INC_PATH = include concept +STRIP_FROM_INC_PATH = include \ + 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 @@ -197,9 +207,9 @@ MULTILINE_CPP_IS_BRIEF = NO INHERIT_DOCS = YES -# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce a -# new page for each member. If set to NO, the documentation of a member will be -# part of the file/class/namespace that contains it. +# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new +# page for each member. If set to NO, the documentation of a member will be part +# of the file/class/namespace that contains it. # The default value is: NO. SEPARATE_MEMBER_PAGES = NO @@ -220,13 +230,7 @@ TAB_SIZE = 2 # "Side Effects:". You can put \n's in the value part of an alias to insert # newlines. -ALIASES = - -# This tag can be used to specify a number of word-keyword mappings (TCL only). -# A mapping has the form "name=value". For example adding "class=itcl::class" -# will allow you to use the command class in the itcl::class meaning. - -TCL_SUBST = +ALIASES = gudhi_example_link{2}="@ref \2 \"\1/\2\"" # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources # only. Doxygen will then generate output that is more tailored for C. For @@ -261,11 +265,14 @@ OPTIMIZE_OUTPUT_VHDL = NO # 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, -# C#, C, C++, D, PHP, Objective-C, Python, Fortran, VHDL. 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. +# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran: +# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran: +# Fortran. In the later case the parser tries to guess whether the code is fixed +# or free formatted code, this is the default for Fortran type files), VHDL. 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 For files without extension you can use no_extension as a placeholder. +# Note: For files without extension you can use no_extension as a placeholder. # # Note that for custom extensions you also need to set FILE_PATTERNS otherwise # the files are not read by doxygen. @@ -282,10 +289,19 @@ EXTENSION_MAPPING = MARKDOWN_SUPPORT = YES +# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up +# to that level are automatically included in the table of contents, even if +# they do not have an id attribute. +# Note: This feature currently applies only to Markdown headings. +# Minimum value: 0, maximum value: 99, default value: 0. +# This tag requires that the tag MARKDOWN_SUPPORT is set to YES. + +TOC_INCLUDE_HEADINGS = 0 + # 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. +# be prevented in individual cases by putting a % sign in front of the word or +# globally by setting AUTOLINK_SUPPORT to NO. # The default value is: YES. AUTOLINK_SUPPORT = YES @@ -325,13 +341,20 @@ SIP_SUPPORT = NO IDL_PROPERTY_SUPPORT = YES # If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC -# tag is set to YES, then doxygen will reuse the documentation of the first +# tag is set to YES then doxygen will reuse the documentation of the first # member in the group (if any) for the other members of the group. By default # all members of a group must be documented explicitly. # The default value is: NO. DISTRIBUTE_GROUP_DOC = NO +# If one adds a struct or class to a group and this option is enabled, then also +# any nested class or struct is added to the same group. By default this option +# is disabled and one has to add nested compounds explicitly via \ingroup. +# The default value is: NO. + +GROUP_NESTED_COMPOUNDS = NO + # Set the SUBGROUPING tag to YES to allow class member groups of the same type # (for instance a group of public functions) to be put as a subgroup of that # type (e.g. under the Public Functions section). Set it to NO to prevent @@ -390,7 +413,7 @@ LOOKUP_CACHE_SIZE = 0 # Build related configuration options #--------------------------------------------------------------------------- -# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in # documentation are documented, even if no documentation was available. Private # class members and static file members will be hidden unless the # EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. @@ -400,35 +423,35 @@ LOOKUP_CACHE_SIZE = 0 EXTRACT_ALL = NO -# If the EXTRACT_PRIVATE tag is set to YES all private members of a class will +# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will # be included in the documentation. # The default value is: NO. EXTRACT_PRIVATE = NO -# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal +# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal # scope will be included in the documentation. # The default value is: NO. EXTRACT_PACKAGE = NO -# If the EXTRACT_STATIC tag is set to YES all static members of a file will be +# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be # included in the documentation. # The default value is: NO. EXTRACT_STATIC = NO -# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) defined -# locally in source files will be included in the documentation. If set to NO +# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined +# locally in source files will be included in the documentation. If set to NO, # only classes defined in header files are included. Does not have any effect # for Java sources. # The default value is: YES. EXTRACT_LOCAL_CLASSES = NO -# This flag is only useful for Objective-C code. When set to YES local methods, +# This flag is only useful for Objective-C code. If set to YES, local methods, # which are defined in the implementation section but not in the interface are -# included in the documentation. If set to NO only methods in the interface are +# included in the documentation. If set to NO, only methods in the interface are # included. # The default value is: NO. @@ -453,21 +476,21 @@ HIDE_UNDOC_MEMBERS = YES # If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all # undocumented classes that are normally visible in the class hierarchy. If set -# to NO these classes will be included in the various overviews. This option has -# no effect if EXTRACT_ALL is enabled. +# to NO, these classes will be included in the various overviews. This option +# has no effect if EXTRACT_ALL is enabled. # The default value is: NO. HIDE_UNDOC_CLASSES = YES # If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend -# (class|struct|union) declarations. If set to NO these declarations will be +# (class|struct|union) declarations. If set to NO, these declarations will be # included in the documentation. # The default value is: NO. HIDE_FRIEND_COMPOUNDS = NO # If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any -# documentation blocks found inside the body of a function. If set to NO these +# documentation blocks found inside the body of a function. If set to NO, these # blocks will be appended to the function's detailed documentation block. # The default value is: NO. @@ -481,7 +504,7 @@ HIDE_IN_BODY_DOCS = NO INTERNAL_DOCS = NO # If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file -# names in lower-case letters. If set to YES upper-case letters are also +# names in lower-case letters. If set to YES, upper-case letters are also # allowed. This is useful if you have classes or files whose names only differ # in case and if your file system supports case sensitive file names. Windows # and Mac users are advised to set this option to NO. @@ -490,12 +513,19 @@ INTERNAL_DOCS = NO CASE_SENSE_NAMES = NO # If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with -# their full class and namespace scopes in the documentation. If set to YES the +# their full class and namespace scopes in the documentation. If set to YES, the # scope will be hidden. # The default value is: NO. HIDE_SCOPE_NAMES = NO +# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will +# append additional text to a page's title, such as Class Reference. If set to +# YES the compound reference will be hidden. +# The default value is: NO. + +HIDE_COMPOUND_REFERENCE= NO + # If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of # the files that are included by a file in the documentation of that file. # The default value is: YES. @@ -523,14 +553,14 @@ INLINE_INFO = YES # If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the # (detailed) documentation of file and class members alphabetically by member -# name. If set to NO the members will appear in declaration order. +# name. If set to NO, the members will appear in declaration order. # The default value is: YES. SORT_MEMBER_DOCS = YES # If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief # descriptions of file, namespace and class members alphabetically by member -# name. If set to NO the members will appear in declaration order. Note that +# name. If set to NO, the members will appear in declaration order. Note that # this will also influence the order of the classes in the class list. # The default value is: NO. @@ -575,27 +605,25 @@ SORT_BY_SCOPE_NAME = NO STRICT_PROTO_MATCHING = NO -# The GENERATE_TODOLIST tag can be used to enable ( YES) or disable ( NO) the -# todo list. This list is created by putting \todo commands in the -# documentation. +# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo +# list. This list is created by putting \todo commands in the documentation. # The default value is: YES. GENERATE_TODOLIST = NO -# The GENERATE_TESTLIST tag can be used to enable ( YES) or disable ( NO) the -# test list. This list is created by putting \test commands in the -# documentation. +# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test +# list. This list is created by putting \test commands in the documentation. # The default value is: YES. GENERATE_TESTLIST = NO -# The GENERATE_BUGLIST tag can be used to enable ( YES) or disable ( NO) the bug +# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug # list. This list is created by putting \bug commands in the documentation. # The default value is: YES. GENERATE_BUGLIST = NO -# The GENERATE_DEPRECATEDLIST tag can be used to enable ( YES) or disable ( NO) +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) # the deprecated list. This list is created by putting \deprecated commands in # the documentation. # The default value is: YES. @@ -620,8 +648,8 @@ ENABLED_SECTIONS = MAX_INITIALIZER_LINES = 30 # Set the SHOW_USED_FILES tag to NO to disable the list of files generated at -# the bottom of the documentation of classes and structs. If set to YES the list -# will mention the files that were used to generate the documentation. +# the bottom of the documentation of classes and structs. If set to YES, the +# list will mention the files that were used to generate the documentation. # The default value is: YES. SHOW_USED_FILES = YES @@ -669,12 +697,10 @@ LAYOUT_FILE = # 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. Do not use file names with spaces, bibtex cannot handle them. See -# also \cite for info how to create references. +# search path. See also \cite for info how to create references. -CITE_BIB_FILES = biblio/bibliography.bib \ - biblio/how_to_cite_cgal.bib \ - biblio/how_to_cite_gudhi.bib +CITE_BIB_FILES = @CMAKE_SOURCE_DIR@/biblio/bibliography.bib \ + @CMAKE_SOURCE_DIR@/biblio/how_to_cite_gudhi.bib #--------------------------------------------------------------------------- # Configuration options related to warning and progress messages @@ -685,10 +711,10 @@ CITE_BIB_FILES = 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 +# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES # this implies that the warnings are on. # # Tip: Turn warnings on while writing the documentation. @@ -696,7 +722,7 @@ QUIET = NO WARNINGS = YES -# If the WARN_IF_UNDOCUMENTED tag is set to YES, then doxygen will generate +# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate # warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag # will automatically be disabled. # The default value is: YES. @@ -713,12 +739,18 @@ WARN_IF_DOC_ERROR = YES # This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that # are documented, but have no documentation for their parameters or return -# value. If set to NO doxygen will only warn about wrong or incomplete parameter -# documentation, but not about the absence of documentation. +# value. If set to NO, doxygen will only warn about wrong or incomplete +# parameter documentation, but not about the absence of documentation. # The default value is: NO. WARN_NO_PARAMDOC = NO +# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when +# a warning is encountered. +# The default value is: NO. + +WARN_AS_ERROR = NO + # The WARN_FORMAT tag determines the format of the warning messages that doxygen # can produce. The string should contain the $file, $line, and $text tags, which # will be replaced by the file and line number from which the warning originated @@ -733,7 +765,7 @@ WARN_FORMAT = "$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 @@ -742,10 +774,10 @@ WARN_LOGFILE = # The INPUT tag is used to specify the files and/or directories that contain # documented source files. You may enter file names like myfile.cpp or # directories like /usr/src/myproject. Separate the files or directories with -# spaces. +# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING # Note: If this tag is empty the current directory is searched. -INPUT = +INPUT = @CMAKE_SOURCE_DIR@ # This tag can be used to specify the character encoding of the source files # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses @@ -758,14 +790,30 @@ INPUT_ENCODING = UTF-8 # If the value of the INPUT tag contains directories, you can use the # FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and -# *.h) to filter out the source-files in the directories. If left blank the -# following patterns are tested:*.c, *.cc, *.cxx, *.cpp, *.c++, *.java, *.ii, -# *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp, -# *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown, -# *.md, *.mm, *.dox, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf, -# *.qsf, *.as and *.js. - -FILE_PATTERNS = +# *.h) to filter out the source-files in the directories. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# read by doxygen. +# +# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp, +# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, +# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, +# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, +# *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf and *.qsf. + +FILE_PATTERNS = *.c \ + *.cc \ + *.cxx \ + *.cpp \ + *.c++ \ + *.h \ + *.hh \ + *.hxx \ + *.hpp \ + *.h++ \ + *.md \ + *.mm \ # The RECURSIVE tag can be used to specify whether or not subdirectories should # be searched for input files as well. @@ -780,12 +828,14 @@ RECURSIVE = YES # Note that relative paths are relative to the directory from which doxygen is # run. -EXCLUDE = data/ \ - example/ \ - GudhUI/ \ - cmake/ \ - python/ \ - README.md +EXCLUDE = @CMAKE_SOURCE_DIR@/data/ \ + @CMAKE_SOURCE_DIR@/ext/ \ + @CMAKE_SOURCE_DIR@/README.md \ + @CMAKE_SOURCE_DIR@/.github \ + @CMAKE_CURRENT_BINARY_DIR@ \ + @GUDHI_DOXYGEN_SOURCE_PREFIX@/GudhUI/ \ + @GUDHI_DOXYGEN_SOURCE_PREFIX@/cmake/ \ + @GUDHI_DOXYGEN_SOURCE_PREFIX@/python/ # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or # directories that are symbolic links (a Unix file system feature) are excluded @@ -801,7 +851,7 @@ EXCLUDE_SYMLINKS = NO # Note that the wildcards are matched against the file with absolute path, so to # exclude all test directories for example use the pattern */test/* -EXCLUDE_PATTERNS = */utilities/*/*.md +EXCLUDE_PATTERNS = @GUDHI_DOXYGEN_SOURCE_PREFIX@/@GUDHI_DOXYGEN_UTILS_PATH@/*.md # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names # (namespaces, classes, functions, etc.) that should be excluded from the @@ -818,17 +868,16 @@ EXCLUDE_SYMBOLS = # that contain example code fragments that are included (see the \include # command). -EXAMPLE_PATH = biblio/ \ - example/ \ - utilities/ \ - data/ +EXAMPLE_PATH = @CMAKE_SOURCE_DIR@ \ + @CMAKE_SOURCE_DIR@/data/ \ + @GUDHI_DOXYGEN_EXAMPLE_PATH@ # If the value of the EXAMPLE_PATH tag contains directories, you can use the # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and # *.h) to filter out the source-files in the directories. If left blank all # files are included. -EXAMPLE_PATTERNS = +EXAMPLE_PATTERNS = # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be # searched for input files to be used with the \include or \dontinclude commands @@ -857,6 +906,10 @@ IMAGE_PATH = @GUDHI_DOXYGEN_IMAGE_PATH@ # Note that the filter must not add or remove lines; it is applied before the # code is scanned, but not when the output code is generated. If lines are added # or removed, the anchors will not be placed correctly. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. INPUT_FILTER = @@ -866,11 +919,15 @@ INPUT_FILTER = # (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how # filters are used. If the FILTER_PATTERNS tag is empty or if none of the # patterns match the file name, INPUT_FILTER is applied. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. FILTER_PATTERNS = # If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using -# INPUT_FILTER ) will also be used to filter the input files that are used for +# INPUT_FILTER) will also be used to filter the input files that are used for # producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). # The default value is: NO. @@ -889,7 +946,7 @@ FILTER_SOURCE_PATTERNS = # (index.html). This can be useful if you have a project on for instance GitHub # and want to reuse the introduction page also for the doxygen output. -USE_MDFILE_AS_MAINPAGE = doc/common/main_page.md +USE_MDFILE_AS_MAINPAGE = @GUDHI_DOXYGEN_COMMON_DOC_PATH@/main_page.md #--------------------------------------------------------------------------- # Configuration options related to source browsing @@ -930,7 +987,7 @@ REFERENCED_BY_RELATION = NO REFERENCES_RELATION = NO # If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set -# to YES, then the hyperlinks from functions in REFERENCES_RELATION and +# to YES then the hyperlinks from functions in REFERENCES_RELATION and # REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will # link to the documentation. # The default value is: YES. @@ -988,13 +1045,6 @@ VERBATIM_HEADERS = YES ALPHABETICAL_INDEX = YES -# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in -# which the alphabetical index list will be split. -# Minimum value: 1, maximum value: 20, default value: 5. -# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. - -COLS_IN_ALPHA_INDEX = 5 - # In case all classes in a project start with a common prefix, all classes will # be put under the same header in the alphabetical index. The IGNORE_PREFIX tag # can be used to specify a prefix (or a list of prefixes) that should be ignored @@ -1007,7 +1057,7 @@ IGNORE_PREFIX = # Configuration options related to the HTML output #--------------------------------------------------------------------------- -# If the GENERATE_HTML tag is set to YES doxygen will generate HTML output +# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output # The default value is: YES. GENERATE_HTML = YES @@ -1045,7 +1095,7 @@ HTML_FILE_EXTENSION = .html # of the possible markers and block names see the documentation. # This tag requires that the tag GENERATE_HTML is set to YES. -HTML_HEADER = doc/common/header.html +HTML_HEADER = @GUDHI_DOXYGEN_COMMON_DOC_PATH@/header.html # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each # generated HTML page. If the tag is left blank doxygen will generate a standard @@ -1055,7 +1105,7 @@ HTML_HEADER = doc/common/header.html # that doxygen normally uses. # This tag requires that the tag GENERATE_HTML is set to YES. -HTML_FOOTER = doc/common/footer.html +HTML_FOOTER = @GUDHI_DOXYGEN_COMMON_DOC_PATH@/footer.html # 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 @@ -1067,18 +1117,20 @@ HTML_FOOTER = doc/common/footer.html # obsolete. # This tag requires that the tag GENERATE_HTML is set to YES. -HTML_STYLESHEET = doc/common/stylesheet.css +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 +# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# cascading style sheets that are 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. For an example -# see the documentation. +# standard style sheet and is therefore more robust against future updates. +# Doxygen will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). For an example see the documentation. # This tag requires that the tag GENERATE_HTML is set to YES. -HTML_EXTRA_STYLESHEET = +HTML_EXTRA_STYLESHEET = @GUDHI_DOXYGEN_COMMON_DOC_PATH@/stylesheet.css # 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 @@ -1090,8 +1142,13 @@ HTML_EXTRA_STYLESHEET = HTML_EXTRA_FILES = +# Default here is AUTO_LIGHT which means "Automatically set the mode according +# to the user preference, use light mode if no preference is set". +# Force it to LIGHT (white), as the rest of the documentation is white. +HTML_COLORSTYLE = LIGHT + # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen -# will adjust the colors in the stylesheet and background images according to +# will adjust the colors in the style sheet and background images according to # this color. Hue is specified as an angle on a colorwheel, see # http://en.wikipedia.org/wiki/Hue for more information. For instance the value # 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 @@ -1122,8 +1179,9 @@ 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. -# The default value is: YES. +# to YES can help to show when doxygen was last run and thus if the +# documentation is up to date. +# The default value is: NO. # This tag requires that the tag GENERATE_HTML is set to YES. HTML_TIMESTAMP = YES @@ -1219,28 +1277,29 @@ GENERATE_HTMLHELP = NO CHM_FILE = # The HHC_LOCATION tag can be used to specify the location (absolute path -# including file name) of the HTML help compiler ( hhc.exe). If non-empty +# including file name) of the HTML help compiler (hhc.exe). If non-empty, # doxygen will try to run the HTML help compiler on the generated index.hhp. # The file has to be specified with full path. # This tag requires that the tag GENERATE_HTMLHELP is set to YES. HHC_LOCATION = -# The GENERATE_CHI flag controls if a separate .chi index file is generated ( -# YES) or that it should be included in the master .chm file ( NO). +# The GENERATE_CHI flag controls if a separate .chi index file is generated +# (YES) or that it should be included in the master .chm file (NO). # The default value is: NO. # This tag requires that the tag GENERATE_HTMLHELP is set to YES. GENERATE_CHI = NO -# The CHM_INDEX_ENCODING is used to encode HtmlHelp index ( hhk), content ( hhc) +# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) # and project file content. # This tag requires that the tag GENERATE_HTMLHELP is set to YES. CHM_INDEX_ENCODING = -# The BINARY_TOC flag controls whether a binary table of contents is generated ( -# YES) or a normal table of contents ( NO) in the .chm file. +# The BINARY_TOC flag controls whether a binary table of contents is generated +# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it +# enables the Previous and Next buttons. # The default value is: NO. # This tag requires that the tag GENERATE_HTMLHELP is set to YES. @@ -1353,7 +1412,7 @@ DISABLE_INDEX = YES # index structure (just like the one that is generated for HTML Help). For this # to work a browser that supports JavaScript, DHTML, CSS and frames is required # (i.e. any modern browser). Windows users are probably better off using the -# HTML help feature. Via custom stylesheets (see HTML_EXTRA_STYLESHEET) one can +# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can # further fine-tune the look of the index. As an example, the default style # sheet generated by doxygen has an example that shows how to put an image at # the root of the tree instead of the PROJECT_NAME. Since the tree basically has @@ -1381,7 +1440,7 @@ ENUM_VALUES_PER_LINE = 4 TREEVIEW_WIDTH = 250 -# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open links to +# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to # external symbols imported via tag files in a separate window. # The default value is: NO. # This tag requires that the tag GENERATE_HTML is set to YES. @@ -1397,20 +1456,9 @@ 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 directory before the changes have effect. -# The default value is: YES. -# This tag requires that the tag GENERATE_HTML is set to YES. - -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 have LaTeX +# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX # installed or if you want to formulas look prettier in the HTML output. When # enabled you may also need to install MathJax separately and configure the path # to it using the MATHJAX_RELPATH option. @@ -1419,6 +1467,17 @@ FORMULA_TRANSPARENT = YES USE_MATHJAX = YES +# With MATHJAX_VERSION it is possible to specify the MathJax version to be used. +# Note that the different versions of MathJax have different requirements with +# regards to the different settings, so it is possible that also other MathJax +# settings have to be changed when switching between the different MathJax +# versions. +# Possible values are: MathJax_2 and MathJax_3. +# The default value is: MathJax_2. +# This tag requires that the tag USE_MATHJAX is set to YES. + +@GUDHI_DOXYGEN_MATHJAX_VERSION@ + # When MathJax is enabled you can set the default output format to be used for # the MathJax output. See the MathJax site (see: # http://docs.mathjax.org/en/latest/output.html) for more details. @@ -1440,14 +1499,14 @@ MATHJAX_FORMAT = HTML-CSS # The default value is: http://cdn.mathjax.org/mathjax/latest. # This tag requires that the tag USE_MATHJAX is set to YES. -MATHJAX_RELPATH = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2 +MATHJAX_RELPATH = # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax # extension names that should be enabled during MathJax rendering. For example # MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols # This tag requires that the tag USE_MATHJAX is set to YES. -MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols +MATHJAX_EXTENSIONS = @GUDHI_DOXYGEN_MATHJAX_EXTENSIONS@ # The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces # of code that will be used on startup of the MathJax code. See the MathJax site @@ -1480,11 +1539,11 @@ SEARCHENGINE = YES # When the SERVER_BASED_SEARCH tag is enabled the search engine will be # implemented using a web server instead of a web client using Javascript. There -# are two flavours of web server based searching 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 section "External Indexing and Searching" for details. +# are two flavors of web server based searching 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 section +# "External Indexing and Searching" for details. # The default value is: NO. # This tag requires that the tag SEARCHENGINE is set to YES. @@ -1496,7 +1555,7 @@ SERVER_BASED_SEARCH = NO # 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 +# Doxygen ships with an example indexer (doxyindexer) and search engine # (doxysearch.cgi) which are based on the open source search engine library # Xapian (see: http://xapian.org/). # @@ -1509,7 +1568,7 @@ EXTERNAL_SEARCH = NO # The SEARCHENGINE_URL should point to a search engine hosted by a web server # which will return the search results when EXTERNAL_SEARCH is enabled. # -# Doxygen ships with an example indexer ( doxyindexer) and search engine +# Doxygen ships with an example indexer (doxyindexer) and search engine # (doxysearch.cgi) which are based on the open source search engine library # Xapian (see: http://xapian.org/). See the section "External Indexing and # Searching" for details. @@ -1547,7 +1606,7 @@ EXTRA_SEARCH_MAPPINGS = # Configuration options related to the LaTeX output #--------------------------------------------------------------------------- -# If the GENERATE_LATEX tag is set to YES doxygen will generate LaTeX output. +# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output. # The default value is: YES. GENERATE_LATEX = NO @@ -1578,7 +1637,7 @@ LATEX_CMD_NAME = latex MAKEINDEX_CMD_NAME = makeindex -# If the COMPACT_LATEX tag is set to YES doxygen generates more compact LaTeX +# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX # documents. This may be useful for small projects and may help to save some # trees in general. # The default value is: NO. @@ -1596,13 +1655,18 @@ COMPACT_LATEX = NO PAPER_TYPE = a4 # The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names -# that should be included in the LaTeX output. To get the times font for -# instance you can specify -# EXTRA_PACKAGES=times +# that should be included in the LaTeX output. The package can be specified just +# by its name or with the correct syntax as to be used with the LaTeX +# \usepackage command. To get the times font for instance you can specify : +# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times} +# To use the option intlimits with the amsmath package you can specify: +# EXTRA_PACKAGES=[intlimits]{amsmath} # If left blank no extra packages will be included. # This tag requires that the tag GENERATE_LATEX is set to YES. -EXTRA_PACKAGES = amsfonts amsmath amssymb +EXTRA_PACKAGES = amsfonts \ + amsmath \ + amssymb # The LATEX_HEADER tag can be used to specify a personal LaTeX header for the # generated LaTeX document. The header should contain everything until the first @@ -1612,23 +1676,36 @@ EXTRA_PACKAGES = amsfonts amsmath amssymb # # Note: Only use a user-defined header if you know what you are doing! The # following commands have a special meaning inside the header: $title, -# $datetime, $date, $doxygenversion, $projectname, $projectnumber. Doxygen will -# replace them by respectively the title of the page, the current date and time, -# only the current date, the version number of doxygen, the project name (see -# PROJECT_NAME), or the project number (see PROJECT_NUMBER). +# $datetime, $date, $doxygenversion, $projectname, $projectnumber, +# $projectbrief, $projectlogo. Doxygen will replace $title with the empty +# string, for the replacement values of the other commands the user is referred +# to HTML_HEADER. # This tag requires that the tag GENERATE_LATEX is set to YES. LATEX_HEADER = # The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for the # generated LaTeX document. The footer should contain everything after the last -# chapter. If it is left blank doxygen will generate a standard footer. +# chapter. If it is left blank doxygen will generate a standard footer. See +# LATEX_HEADER for more information on how to generate a default footer and what +# special commands can be used inside the footer. # # Note: Only use a user-defined footer if you know what you are doing! # This tag requires that the tag GENERATE_LATEX is set to YES. LATEX_FOOTER = +# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# LaTeX style sheets that are included after the standard style sheets created +# by doxygen. Using this option one can overrule certain style aspects. Doxygen +# will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_EXTRA_STYLESHEET = + # The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or # other source files which should be copied to the LATEX_OUTPUT output # directory. Note that the files will be copied as-is; there are no commands or @@ -1646,8 +1723,8 @@ LATEX_EXTRA_FILES = PDF_HYPERLINKS = YES -# If the LATEX_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate -# the PDF file directly from the LaTeX files. Set this option to YES to get a +# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate +# the PDF file directly from the LaTeX files. Set this option to YES, to get a # higher quality PDF documentation. # The default value is: YES. # This tag requires that the tag GENERATE_LATEX is set to YES. @@ -1670,16 +1747,6 @@ LATEX_BATCHMODE = NO LATEX_HIDE_INDICES = NO -# If the LATEX_SOURCE_CODE tag 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. -# The default value is: NO. -# This tag requires that the tag GENERATE_LATEX is set to YES. - -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. See # http://en.wikipedia.org/wiki/BibTeX and \cite for more info. @@ -1688,11 +1755,19 @@ LATEX_SOURCE_CODE = NO LATEX_BIB_STYLE = plain +# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated +# 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. +# The default value is: NO. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_TIMESTAMP = NO + #--------------------------------------------------------------------------- # Configuration options related to the RTF output #--------------------------------------------------------------------------- -# If the GENERATE_RTF tag is set to YES doxygen will generate RTF output. The +# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The # RTF output is optimized for Word 97 and may not look too pretty with other RTF # readers/editors. # The default value is: NO. @@ -1707,7 +1782,7 @@ GENERATE_RTF = NO RTF_OUTPUT = rtf -# If the COMPACT_RTF tag is set to YES doxygen generates more compact RTF +# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF # documents. This may be useful for small projects and may help to save some # trees in general. # The default value is: NO. @@ -1748,7 +1823,7 @@ RTF_EXTENSIONS_FILE = # Configuration options related to the man page output #--------------------------------------------------------------------------- -# If the GENERATE_MAN tag is set to YES doxygen will generate man pages for +# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for # classes and files. # The default value is: NO. @@ -1772,6 +1847,13 @@ MAN_OUTPUT = man MAN_EXTENSION = .3 +# The MAN_SUBDIR tag determines the name of the directory created within +# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by +# MAN_EXTENSION with the initial . removed. +# This tag requires that the tag GENERATE_MAN is set to YES. + +MAN_SUBDIR = + # If the MAN_LINKS tag is set to YES and doxygen generates man output, then it # will generate one additional man file for each entity documented in the real # man page(s). These additional files only source the real man page, but without @@ -1785,7 +1867,7 @@ MAN_LINKS = NO # Configuration options related to the XML output #--------------------------------------------------------------------------- -# If the GENERATE_XML tag is set to YES doxygen will generate an XML file that +# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that # captures the structure of the code including all documentation. # The default value is: NO. @@ -1799,7 +1881,7 @@ GENERATE_XML = NO XML_OUTPUT = xml -# If the XML_PROGRAMLISTING tag is set to YES doxygen will dump the program +# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program # listings (including syntax highlighting and cross-referencing information) to # the XML output. Note that enabling this will significantly increase the size # of the XML output. @@ -1812,7 +1894,7 @@ XML_PROGRAMLISTING = YES # Configuration options related to the DOCBOOK output #--------------------------------------------------------------------------- -# If the GENERATE_DOCBOOK tag is set to YES doxygen will generate Docbook files +# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files # that can be used to generate PDF. # The default value is: NO. @@ -1830,10 +1912,10 @@ DOCBOOK_OUTPUT = docbook # Configuration options for the AutoGen Definitions output #--------------------------------------------------------------------------- -# If the GENERATE_AUTOGEN_DEF tag is set to YES doxygen will generate an AutoGen -# Definitions (see http://autogen.sf.net) file that captures the structure of -# the code including all documentation. Note that this feature is still -# experimental and incomplete at the moment. +# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an +# AutoGen Definitions (see http://autogen.sf.net) file that captures the +# structure of the code including all documentation. Note that this feature is +# still experimental and incomplete at the moment. # The default value is: NO. GENERATE_AUTOGEN_DEF = NO @@ -1842,7 +1924,7 @@ GENERATE_AUTOGEN_DEF = NO # Configuration options related to the Perl module output #--------------------------------------------------------------------------- -# If the GENERATE_PERLMOD tag is set to YES doxygen will generate a Perl module +# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module # file that captures the structure of the code including all documentation. # # Note that this feature is still experimental and incomplete at the moment. @@ -1850,7 +1932,7 @@ GENERATE_AUTOGEN_DEF = NO GENERATE_PERLMOD = NO -# If the PERLMOD_LATEX tag is set to YES doxygen will generate the necessary +# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary # Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI # output from the Perl module output. # The default value is: NO. @@ -1858,9 +1940,9 @@ GENERATE_PERLMOD = NO PERLMOD_LATEX = NO -# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be nicely +# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely # formatted so it can be parsed by a human reader. This is useful if you want to -# understand what is going on. On the other hand, if this tag is set to NO the +# understand what is going on. On the other hand, if this tag is set to NO, the # size of the Perl module output will be much smaller and Perl will parse it # just the same. # The default value is: YES. @@ -1880,14 +1962,14 @@ PERLMOD_MAKEVAR_PREFIX = # Configuration options related to the preprocessor #--------------------------------------------------------------------------- -# If the ENABLE_PREPROCESSING tag is set to YES doxygen will evaluate all +# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all # C-preprocessor directives found in the sources and include files. # The default value is: YES. ENABLE_PREPROCESSING = YES -# If the MACRO_EXPANSION tag is set to YES doxygen will expand all macro names -# in the source code. If set to NO only conditional compilation will be +# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names +# in the source code. If set to NO, only conditional compilation will be # performed. Macro expansion can be done in a controlled way by setting # EXPAND_ONLY_PREDEF to YES. # The default value is: NO. @@ -1903,7 +1985,7 @@ MACRO_EXPANSION = YES EXPAND_ONLY_PREDEF = YES -# If the SEARCH_INCLUDES tag is set to YES the includes files in the +# If the SEARCH_INCLUDES tag is set to YES, the include files in the # INCLUDE_PATH will be searched if a #include is found. # The default value is: YES. # This tag requires that the tag ENABLE_PREPROCESSING is set to YES. @@ -1945,9 +2027,9 @@ PREDEFINED = protected=private EXPAND_AS_DEFINED = # If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will -# remove all refrences to function-like macros that are alone on a line, have an -# all uppercase name, and do not end with a semicolon. Such function macros are -# typically used for boiler-plate code, and will confuse the parser if not +# remove all references to function-like macros that are alone on a line, have +# an all uppercase name, and do not end with a semicolon. Such function macros +# are typically used for boiler-plate code, and will confuse the parser if not # removed. # The default value is: YES. # This tag requires that the tag ENABLE_PREPROCESSING is set to YES. @@ -1967,7 +2049,7 @@ SKIP_FUNCTION_MACROS = YES # where loc1 and loc2 can be relative or absolute paths or URLs. See the # section "Linking to external documentation" for more information about the use # of tag files. -# Note: Each tag file must have an unique name (where the name does NOT include +# Note: Each tag file must have a unique name (where the name does NOT include # the path). If a tag file is not located in the directory in which doxygen is # run, you must also specify the path to the tagfile here. @@ -1979,53 +2061,32 @@ TAGFILES = GENERATE_TAGFILE = -# If the ALLEXTERNALS tag is set to YES all external class will be listed in the -# class index. If set to NO only the inherited external classes will be listed. +# If the ALLEXTERNALS tag is set to YES, all external class will be listed in +# the class index. If set to NO, only the inherited external classes will be +# listed. # The default value is: NO. ALLEXTERNALS = NO -# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed in -# the modules index. If set to NO, only the current project's groups will be +# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed +# in the modules index. If set to NO, only the current project's groups will be # listed. # The default value is: YES. EXTERNAL_GROUPS = YES -# If the EXTERNAL_PAGES tag is set to YES all external pages will be listed in +# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in # the related pages index. If set to NO, only the current project's pages will # be listed. # The default value is: YES. EXTERNAL_PAGES = YES -# The PERL_PATH should be the absolute path and name of the perl script -# interpreter (i.e. the result of 'which perl'). -# The default file (with absolute path) is: /usr/bin/perl. - -PERL_PATH = /usr/bin/perl - #--------------------------------------------------------------------------- # Configuration options related to the dot tool #--------------------------------------------------------------------------- -# If the CLASS_DIAGRAMS tag is set to YES doxygen will generate a class diagram -# (in HTML 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. -# The default value is: YES. - -CLASS_DIAGRAMS = NO - -# 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 -# documentation. The MSCGEN_PATH tag allows you to specify the directory where -# the mscgen tool resides. If left empty the tool is assumed to be found in the -# default search path. - -MSCGEN_PATH = +@GUDHI_DOXYGEN_CLASS_DIAGRAMS@ # You can include diagrams made with dia in doxygen documentation. Doxygen will # then run dia to produce the diagram and insert it in the documentation. The @@ -2034,7 +2095,7 @@ MSCGEN_PATH = DIA_PATH = -# If set to YES, the inheritance and collaboration graphs will hide inheritance +# If set to YES the inheritance and collaboration graphs will hide inheritance # and usage relations if the target is undocumented or is not a class. # The default value is: YES. @@ -2045,7 +2106,7 @@ HIDE_UNDOC_RELATIONS = YES # http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent # Bell Labs. The other options in this section have no effect if this option is # set to NO -# The default value is: NO. +# The default value is: YES. HAVE_DOT = YES @@ -2059,26 +2120,38 @@ HAVE_DOT = YES DOT_NUM_THREADS = 0 -# When you want a differently looking font n the dot files that doxygen -# generates 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. -# The default value is: Helvetica. +# DOT_COMMON_ATTR is common attributes for nodes, edges and labels of +# subgraphs. When you want a differently looking font in the dot files that +# doxygen generates you can specify fontname, fontcolor and fontsize attributes. +# For details please see <a href=https://graphviz.org/doc/info/attrs.html>Node, +# Edge and Graph Attributes specification</a> 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. Default graphviz fontsize is 14. +# The default value is: fontname=Helvetica,fontsize=10. # This tag requires that the tag HAVE_DOT is set to YES. -DOT_FONTNAME = Helvetica +DOT_COMMON_ATTR = "fontname=Helvetica,fontsize=10" -# The DOT_FONTSIZE tag can be used to set the size (in points) of the font of -# dot graphs. -# Minimum value: 4, maximum value: 24, default value: 10. +# DOT_EDGE_ATTR is concatenated with DOT_COMMON_ATTR. For elegant style you can +# add 'arrowhead=open, arrowtail=open, arrowsize=0.5'. <a +# href=https://graphviz.org/doc/info/arrows.html>Complete documentation about +# arrows shapes.</a> +# The default value is: labelfontname=Helvetica,labelfontsize=10. # This tag requires that the tag HAVE_DOT is set to YES. -DOT_FONTSIZE = 10 +DOT_EDGE_ATTR = "labelfontname=Helvetica,labelfontsize=10" -# By default doxygen will tell dot to use the default font as specified with -# DOT_FONTNAME. If you specify a different font using DOT_FONTNAME you can set -# the path where dot can find it using this tag. +# DOT_NODE_ATTR is concatenated with DOT_COMMON_ATTR. For view without boxes +# around nodes set 'shape=plain' or 'shape=plaintext' <a +# href=https://www.graphviz.org/doc/info/shapes.html>Shapes specification</a> +# The default value is: shape=box,height=0.2,width=0.4. +# This tag requires that the tag HAVE_DOT is set to YES. + +DOT_NODE_ATTR = "shape=box,height=0.2,width=0.4" + +# You can set the path where dot can find font specified with fontname in +# DOT_COMMON_ATTR and others dot attributes. # This tag requires that the tag HAVE_DOT is set to YES. DOT_FONTPATH = @@ -2107,7 +2180,7 @@ COLLABORATION_GRAPH = NO GROUP_GRAPHS = YES -# If the UML_LOOK tag is set to YES doxygen will generate inheritance and +# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and # collaboration diagrams in a style similar to the OMG's Unified Modeling # Language. # The default value is: NO. @@ -2159,7 +2232,8 @@ INCLUDED_BY_GRAPH = NO # # Note that enabling this option will significantly increase the time of a run. # So in most cases it will be better to enable call graphs for selected -# functions only using the \callgraph command. +# functions only using the \callgraph command. Disabling a call graph can be +# accomplished by means of the command \hidecallgraph. # The default value is: NO. # This tag requires that the tag HAVE_DOT is set to YES. @@ -2170,7 +2244,8 @@ CALL_GRAPH = NO # # Note that enabling this option will significantly increase the time of a run. # So in most cases it will be better to enable caller graphs for selected -# functions only using the \callergraph command. +# functions only using the \callergraph command. Disabling a caller graph can be +# accomplished by means of the command \hidecallergraph. # The default value is: NO. # This tag requires that the tag HAVE_DOT is set to YES. @@ -2193,11 +2268,17 @@ GRAPHICAL_HIERARCHY = YES DIRECTORY_GRAPH = YES # The DOT_IMAGE_FORMAT tag can be used to set the image format of the images -# generated by dot. +# generated by dot. For an explanation of the image formats see the section +# output formats in the documentation of the dot tool (Graphviz (see: +# http://www.graphviz.org/)). # Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order # to make the SVG files visible in IE 9+ (other browsers do not have this # requirement). -# Possible values are: png, jpg, gif and svg. +# Possible values are: png, png:cairo, png:cairo:cairo, png:cairo:gd, png:gd, +# png:gd:gd, jpg, jpg:cairo, jpg:cairo:gd, jpg:gd, jpg:gd:gd, gif, gif:cairo, +# gif:cairo:gd, gif:gd, gif:gd:gd, svg, png:gd, png:gd:gd, png:cairo, +# png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and +# png:gdiplus:gdiplus. # The default value is: png. # This tag requires that the tag HAVE_DOT is set to YES. @@ -2240,6 +2321,24 @@ MSCFILE_DIRS = DIAFILE_DIRS = +# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the +# path where java can find the plantuml.jar file. If left blank, it is assumed +# PlantUML is not used or called during a preprocessing step. Doxygen will +# generate a warning when it encounters a \startuml command in this case and +# will not generate output for the diagram. + +PLANTUML_JAR_PATH = + +# When using plantuml, the PLANTUML_CFG_FILE tag can be used to specify a +# configuration file for plantuml. + +PLANTUML_CFG_FILE = + +# When using plantuml, the specified paths are searched for files specified by +# the !include statement in a plantuml block. + +PLANTUML_INCLUDE_PATH = + # The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes # that will be shown in the graph. If the number of nodes in a graph becomes # larger than this value, doxygen will truncate the graph, which is visualized @@ -2264,19 +2363,7 @@ DOT_GRAPH_MAX_NODES = 50 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). -# The default value is: NO. -# This tag requires that the tag HAVE_DOT is set to YES. - -DOT_TRANSPARENT = NO - -# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# Set the DOT_MULTI_TARGETS tag to YES to 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) support # this, this feature is disabled by default. @@ -2293,7 +2380,7 @@ DOT_MULTI_TARGETS = YES GENERATE_LEGEND = YES -# If the DOT_CLEANUP tag is set to YES doxygen will remove the intermediate dot +# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate dot # files that are used to generate the various graphs. # The default value is: YES. # This tag requires that the tag HAVE_DOT is set to YES. |