Bump Doxygen to 1.13.0

Should resolve [#24](#24).

Author: pcolby

.github/workflows/docs.yaml

@@ -6,7 +6,7 @@ permissions:
   contents: read
 
 env:
-  DOXYGEN_VERSION: 1.11.0
+  DOXYGEN_VERSION: 1.13.0
 
 jobs:
   generate:

doc/doxyfile.in

@@ -1,4 +1,4 @@
-# Doxyfile 1.12.0
+# Doxyfile 1.13.0
 
 # This file describes the settings to be used by the documentation system
 # Doxygen (www.doxygen.org) for a project.
@@ -51,7 +51,7 @@ PROJECT_NAME           = "${PROJECT_NAME}"
 PROJECT_NUMBER         = "${PROJECT_VERSION}${PROJECT_VERSION_SUFFIX}"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
-# for a project that appears at the top of each page and should give viewer a
+# for a project that appears at the top of each page and should give viewers a
 # quick idea about the purpose of the project. Keep the description short.
 
 PROJECT_BRIEF          = "${DOX_PROJECT_BRIEF}"
@@ -80,7 +80,7 @@ OUTPUT_DIRECTORY       =
 # 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
-# putting all generated files in the same directory would otherwise causes
+# putting all generated files in the same directory would otherwise cause
 # performance problems for the file system. Adapt CREATE_SUBDIRS_LEVEL to
 # control the number of sub-directories.
 # The default value is: NO.
@@ -202,17 +202,17 @@ STRIP_FROM_PATH        =
 STRIP_FROM_INC_PATH    =
 
 # 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
+# less readable) file names. This can be useful if your file system doesn't
 # support long names like on DOS, Mac, or CD-ROM.
 # The default value is: NO.
 
 SHORT_NAMES            = NO
 
 # If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen will interpret the
-# first line (until the first dot) of a Javadoc-style comment as the brief
-# description. If set to NO, the Javadoc-style will behave just like regular Qt-
-# style comments (thus requiring an explicit @brief command for a brief
-# description.)
+# first line (until the first dot, question mark or exclamation mark) of a
+# Javadoc-style comment as the brief description. If set to NO, the Javadoc-
+# style will behave just like regular Qt-style comments (thus requiring an
+# explicit @brief command for a brief description.)
 # The default value is: NO.
 
 JAVADOC_AUTOBRIEF      = NO
@@ -228,9 +228,10 @@ JAVADOC_AUTOBRIEF      = NO
 JAVADOC_BANNER         = NO
 
 # If the QT_AUTOBRIEF tag is set to YES then Doxygen will interpret the first
-# line (until the first dot) of a Qt-style comment as the brief description. If
-# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
-# requiring an explicit \brief command for a brief description.)
+# line (until the first dot, question mark or exclamation mark) of a Qt-style
+# comment as the brief description. If set to NO, the Qt-style will behave just
+# like regular Qt-style comments (thus requiring an explicit \brief command for
+# a brief description.)
 # The default value is: NO.
 
 QT_AUTOBRIEF           = YES
@@ -384,11 +385,20 @@ MARKDOWN_ID_STYLE      = DOXYGEN
 # 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 putting a % sign in front of the word or
-# globally by setting AUTOLINK_SUPPORT to NO.
+# globally by setting AUTOLINK_SUPPORT to NO. Words listed in the
+# AUTOLINK_IGNORE_WORDS tag are excluded from automatic linking.
 # The default value is: YES.
 
 AUTOLINK_SUPPORT       = YES
 
+# This tag specifies a list of words that, when matching the start of a word in
+# the documentation, will suppress auto links generation, if it is enabled via
+# AUTOLINK_SUPPORT. This list does not affect affect links explicitly created
+# using \# or the \link or commands.
+# This tag requires that the tag AUTOLINK_SUPPORT is set to YES.
+
+AUTOLINK_IGNORE_WORDS  =
+
 # 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
@@ -600,6 +610,14 @@ HIDE_UNDOC_MEMBERS     = NO
 
 HIDE_UNDOC_CLASSES     = NO
 
+# If the HIDE_UNDOC_NAMESPACES tag is set to YES, Doxygen will hide all
+# undocumented namespaces that are normally visible in the namespace hierarchy.
+# If set to NO, these namespaces will be included in the various overviews. This
+# option has no effect if EXTRACT_ALL is enabled.
+# The default value is: YES.
+
+HIDE_UNDOC_NAMESPACES  = YES
+
 # If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all friend
 # declarations. If set to NO, these declarations will be included in the
 # documentation.
@@ -984,10 +1002,10 @@ INPUT                  = \
 INPUT_ENCODING         = UTF-8
 
 # This tag can be used to specify the character encoding of the source files
-# that Doxygen parses The INPUT_FILE_ENCODING tag can be used to specify
+# that Doxygen parses. The INPUT_FILE_ENCODING tag can be used to specify
 # character encoding on a per file pattern basis. Doxygen will compare the file
 # name with each pattern and apply the encoding instead of the default
-# INPUT_ENCODING) if there is a match. The character encodings are a list of the
+# INPUT_ENCODING if there is a match. The character encodings are a list of the
 # form: pattern=encoding (like *.php=ISO-8859-1).
 # See also: INPUT_ENCODING for further information on supported encodings.
 
@@ -1139,6 +1157,15 @@ FILTER_SOURCE_PATTERNS =
 
 USE_MDFILE_AS_MAINPAGE = "${CMAKE_SOURCE_DIR}/${DOX_INPUT_DOC}/mainpage.md"
 
+# If the IMPLICIT_DIR_DOCS tag is set to YES, any README.md file found in sub-
+# directories of the project's root, is used as the documentation for that sub-
+# directory, except when the README.md starts with a \dir, \page or \mainpage
+# command. If set to NO, the README.md file needs to start with an explicit \dir
+# command in order to be used as directory documentation.
+# The default value is: YES.
+
+IMPLICIT_DIR_DOCS      = YES
+
 # The Fortran standard specifies that for fixed formatted Fortran code all
 # characters from position 72 are to be considered as comment. A common
 # extension is to allow longer lines before the automatic comment starts. The
@@ -1550,9 +1577,9 @@ DOCSET_PUBLISHER_NAME  = Publisher
 # additional HTML index files: index.hhp, index.hhc, and index.hhk. The
 # index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
 # on Windows. In the beginning of 2021 Microsoft took the original page, with
-# a.o. the download links, offline the HTML help workshop was already many years
-# in maintenance mode). You can download the HTML help workshop from the web
-# archives at Installation executable (see:
+# a.o. the download links, offline (the HTML help workshop was already many
+# years in maintenance mode). You can download the HTML help workshop from the
+# web archives at Installation executable (see:
 # http://web.archive.org/web/20160201063255/http://download.microsoft.com/downlo
 # ad/0/A/9/0A939EF6-E31C-430F-A3DF-DFAE7960D564/htmlhelp.exe).
 #
@@ -1711,7 +1738,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # of each HTML page. A value of NO enables the index and the value YES disables
 # it. Since the tabs in the index contain the same information as the navigation
 # tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
-# The default value is: NO.
+# The default value is: YES.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
 DISABLE_INDEX          = NO
@@ -1728,7 +1755,7 @@ DISABLE_INDEX          = NO
 # shows how to put an image at the root of the tree instead of the PROJECT_NAME.
 # Since the tree basically has the same information as the tab index, you could
 # consider setting DISABLE_INDEX to YES when enabling this option.
-# The default value is: NO.
+# The default value is: YES.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
 GENERATE_TREEVIEW      = YES
@@ -2140,10 +2167,10 @@ LATEX_HIDE_INDICES     = NO
 # The LATEX_BIB_STYLE tag can be used to specify the style to use for the
 # bibliography, e.g. plainnat, or ieeetr. See
 # https://en.wikipedia.org/wiki/BibTeX and \cite for more info.
-# The default value is: plain.
+# The default value is: plainnat.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
-LATEX_BIB_STYLE        = plain
+LATEX_BIB_STYLE        = plainnat
 
 # The LATEX_EMOJI_DIRECTORY tag is used to specify the (relative or absolute)
 # path from which the emoji images will be read. If a relative path is entered,
@@ -2814,6 +2841,12 @@ PLANTUML_CFG_FILE      =
 
 PLANTUML_INCLUDE_PATH  =
 
+# The PLANTUMLFILE_DIRS tag can be used to specify one or more directories that
+# contain PlantUml files that are included in the documentation (see the
+# \plantumlfile command).
+
+PLANTUMLFILE_DIRS      =
+
 # 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