From 070f47e0d583f808608c1ce64b286071e70a59d3 Mon Sep 17 00:00:00 2001
From: jonperdomo <jonperdomodb@gmail.com>
Date: Wed, 13 Sep 2023 13:01:49 -0400
Subject: [PATCH] Update docs

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 rename {docs/doxygen/latex => latex}/swig__wrapper_8cpp_afffa0f94d47fd5cdf487592e5541c61a_icgraph.md5 (100%)
 rename {docs/doxygen/latex => latex}/swig__wrapper_8cpp_afffa0f94d47fd5cdf487592e5541c61a_icgraph.pdf (99%)
 rename {docs/doxygen/latex => latex}/tabu_doxygen.sty (100%)
 rename {docs/doxygen/latex => latex}/test__general_8py.tex (100%)
 rename {docs/doxygen/latex => latex}/tests_2log_8txt.tex (100%)
 rename {docs/doxygen/latex => latex}/train__model_8py.tex (100%)
 rename {docs/doxygen/latex => latex}/types_8h.tex (100%)
 rename {docs/doxygen/latex => latex}/types_8h__dep__incl.md5 (100%)
 rename {docs/doxygen/latex => latex}/types_8h__dep__incl.pdf (99%)
 rename {docs/doxygen/latex => latex}/types_8h__incl.md5 (100%)
 rename {docs/doxygen/latex => latex}/types_8h__incl.pdf (99%)
 rename {docs/doxygen/latex => latex}/types_8h_source.tex (100%)
 rename {docs/doxygen/latex => latex}/utils_8cpp.tex (100%)
 rename {docs/doxygen/latex => latex}/utils_8cpp__incl.md5 (100%)
 rename {docs/doxygen/latex => latex}/utils_8cpp__incl.pdf (99%)
 rename {docs/doxygen/latex => latex}/utils_8cpp_a94bd78faf212464ede8144a4be0e8cf8_icgraph.md5 (100%)
 rename {docs/doxygen/latex => latex}/utils_8cpp_a94bd78faf212464ede8144a4be0e8cf8_icgraph.pdf (99%)
 rename {docs/doxygen/latex => latex}/utils_8h.tex (100%)
 rename {docs/doxygen/latex => latex}/utils_8h__dep__incl.md5 (100%)
 rename {docs/doxygen/latex => latex}/utils_8h__dep__incl.pdf (99%)
 rename {docs/doxygen/latex => latex}/utils_8h__incl.md5 (100%)
 rename {docs/doxygen/latex => latex}/utils_8h__incl.pdf (99%)
 rename {docs/doxygen/latex => latex}/utils_8h_a94bd78faf212464ede8144a4be0e8cf8_icgraph.md5 (100%)
 rename {docs/doxygen/latex => latex}/utils_8h_a94bd78faf212464ede8144a4be0e8cf8_icgraph.pdf (99%)
 rename {docs/doxygen/latex => latex}/utils_8h_source.tex (100%)

diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index a45d8490..f2e8bc21 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -34,4 +34,4 @@ jobs:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         # Default Doxyfile build documentation to docs directory. 
         # Change the directory if changes in Doxyfile
-        publish_dir: ./docs
+        publish_dir: ./html
diff --git a/Doxyfile b/Doxyfile
index 3745711a..ef2f6de3 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -68,7 +68,7 @@ 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/doxygen
+OUTPUT_DIRECTORY       =
 
 # If the CREATE_SUBDIRS tag is set to YES then doxygen will create up to 4096
 # sub-directories (in 2 levels) under the output directory of each output format
diff --git a/docs/Doxyfile.bak b/docs/Doxyfile.bak
deleted file mode 100644
index 691382ab..00000000
--- a/docs/Doxyfile.bak
+++ /dev/null
@@ -1,2580 +0,0 @@
-# Doxyfile 1.8.17
-
-# This file describes the settings to be used by the documentation system
-# doxygen (www.doxygen.org) for a project.
-#
-# All text after a double hash (##) is considered a comment and is placed in
-# front of the TAG it is preceding.
-#
-# All text after a single hash (#) is considered a comment and will be ignored.
-# The format is:
-# TAG = value [value, ...]
-# For lists, items can also be appended using:
-# TAG += value [value, ...]
-# Values that contain spaces should be placed between quotes (\" \").
-
-#---------------------------------------------------------------------------
-# Project related configuration options
-#---------------------------------------------------------------------------
-
-# This tag specifies the encoding used for all characters in the configuration
-# file that follow. The default is UTF-8 which is also the encoding used for all
-# text before the first occurrence of this tag. Doxygen uses libiconv (or the
-# iconv built into libc) for the transcoding. See
-# https://www.gnu.org/software/libiconv/ for the list of possible encodings.
-# The default value is: UTF-8.
-
-DOXYFILE_ENCODING      = UTF-8
-
-# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
-# double-quotes, unless you are using Doxywizard) that should identify the
-# project for which the documentation is generated. This name is used in the
-# title of most generated pages and in a few other places.
-# The default value is: My Project.
-
-PROJECT_NAME           = ContextSV
-
-# 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
-# control system is used.
-
-PROJECT_NUMBER         = 0.0.1
-
-# 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
-# quick idea about the purpose of the project. Keep the description short.
-
-PROJECT_BRIEF          = "Integrative SV calling."
-
-# 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           =
-
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
-# into which the generated documentation will be written. If a relative path is
-# entered, it will be relative to the location where doxygen was started. If
-# left blank the current directory will be used.
-
-OUTPUT_DIRECTORY       = doc/doxygen
-
-# 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
-# putting all generated files in the same directory would otherwise causes
-# performance problems for the file system.
-# The default value is: NO.
-
-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.
-# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese,
-# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States),
-# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian,
-# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages),
-# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian,
-# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian,
-# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish,
-# Ukrainian and Vietnamese.
-# The default value is: English.
-
-OUTPUT_LANGUAGE        = English
-
-# The OUTPUT_TEXT_DIRECTION tag is used to specify the direction in which all
-# documentation generated by doxygen is written. Doxygen will use this
-# information to generate all generated output in the proper direction.
-# Possible values are: None, LTR, RTL and Context.
-# The default value is: None.
-
-OUTPUT_TEXT_DIRECTION  = None
-
-# 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
-# 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
-# brief descriptions will be completely suppressed.
-# The default value is: YES.
-
-REPEAT_BRIEF           = YES
-
-# This tag implements a quasi-intelligent brief description abbreviator that is
-# used to form the text in various listings. Each string in this list, if found
-# as the leading text of the brief description, will be stripped from the text
-# and the result, after processing the whole list, is used as the annotated
-# text. Otherwise, the brief description is used as-is. If left blank, the
-# following values are used ($name is automatically replaced with the name of
-# the entity):The $name class, The $name widget, The $name file, is, provides,
-# specifies, contains, represents, a, an and the.
-
-ABBREVIATE_BRIEF       = "The $name class" \
-                         "The $name widget" \
-                         "The $name file" \
-                         is \
-                         provides \
-                         specifies \
-                         contains \
-                         represents \
-                         a \
-                         an \
-                         the
-
-# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
-# doxygen will generate a detailed section even if there is only a brief
-# description.
-# The default value is: NO.
-
-ALWAYS_DETAILED_SEC    = NO
-
-# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
-# inherited members of a class in the documentation of that class as if those
-# members were ordinary class members. Constructors, destructors and assignment
-# operators of the base classes will not be shown.
-# The default value is: NO.
-
-INLINE_INHERITED_MEMB  = NO
-
-# 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.
-
-FULL_PATH_NAMES        = YES
-
-# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
-# Stripping is 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.
-#
-# Note that you can specify absolute paths here, but also relative paths, which
-# 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        =
-
-# 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
-# header file to include in order to use a class. If left blank only the name of
-# the header file containing the class definition is used. Otherwise one should
-# specify the list of include paths that are normally passed to the compiler
-# using the -I flag.
-
-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
-# 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.)
-# The default value is: NO.
-
-JAVADOC_AUTOBRIEF      = NO
-
-# If the JAVADOC_BANNER tag is set to YES then doxygen will interpret a line
-# such as
-# /***************
-# as being the beginning of a Javadoc-style comment "banner". If set to NO, the
-# Javadoc-style will behave just like regular comments and it will not be
-# interpreted by doxygen.
-# The default value is: 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.)
-# The default value is: NO.
-
-QT_AUTOBRIEF           = NO
-
-# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
-# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
-# a brief description. This used to be the default behavior. The new default is
-# to treat a multi-line C++ comment block as a detailed description. Set this
-# tag to YES if you prefer the old behavior instead.
-#
-# Note that setting this tag to YES also means that rational rose comments are
-# not recognized any more.
-# The default value is: NO.
-
-MULTILINE_CPP_IS_BRIEF = NO
-
-# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
-# documentation from any documented member that it re-implements.
-# The default value is: YES.
-
-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.
-# The default value is: NO.
-
-SEPARATE_MEMBER_PAGES  = NO
-
-# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
-# uses this value to replace tabs by spaces in code fragments.
-# Minimum value: 1, maximum value: 16, default value: 4.
-
-TAB_SIZE               = 4
-
-# This tag can be used to specify a number of aliases that act as commands in
-# the documentation. An alias has the form:
-# name=value
-# For example adding
-# "sideeffect=@par Side Effects:\n"
-# will allow you to put the command \sideeffect (or @sideeffect) in the
-# documentation, which will result in a user-defined paragraph with heading
-# "Side Effects:". You can put \n's in the value part of an alias to insert
-# newlines (in the resulting output). You can put ^^ in the value part of an
-# alias to insert a newline as if a physical newline was in the original file.
-# When you need a literal { or } or , in the value part of an alias you have to
-# escape them by means of a backslash (\), this can lead to conflicts with the
-# commands \{ and \} for these it is advised to use the version @{ and @} or use
-# a double escape (\\{ and \\})
-
-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              =
-
-# 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
-# instance, some of the names that are used will be different. The list of all
-# members will be omitted, etc.
-# The default value is: NO.
-
-OPTIMIZE_OUTPUT_FOR_C  = NO
-
-# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
-# Python sources only. Doxygen will then generate output that is more tailored
-# for that language. For instance, namespaces will be presented as packages,
-# qualified scopes will look different, etc.
-# The default value is: NO.
-
-OPTIMIZE_OUTPUT_JAVA   = NO
-
-# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
-# sources. Doxygen will then generate output that is tailored for Fortran.
-# The default value is: NO.
-
-OPTIMIZE_FOR_FORTRAN   = NO
-
-# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
-# sources. Doxygen will then generate output that is tailored for VHDL.
-# The default value is: NO.
-
-OPTIMIZE_OUTPUT_VHDL   = NO
-
-# Set the OPTIMIZE_OUTPUT_SLICE tag to YES if your project consists of Slice
-# sources only. Doxygen will then generate output that is more tailored for that
-# language. For instance, namespaces will be presented as modules, types will be
-# separated into more groups, etc.
-# The default value is: NO.
-
-OPTIMIZE_OUTPUT_SLICE  = 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, C++, D, PHP, md (Markdown), Objective-C, Python, Slice,
-# 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, tcl. 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 that for custom extensions you also need to set FILE_PATTERNS otherwise
-# the files are not read by doxygen.
-
-EXTENSION_MAPPING      =
-
-# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
-# according to the Markdown format, which allows for more readable
-# documentation. See https://daringfireball.net/projects/markdown/ for details.
-# The output of markdown processing is further processed by doxygen, so you can
-# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
-# case of backward compatibilities issues.
-# The default value is: YES.
-
-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: 5.
-# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
-
-TOC_INCLUDE_HEADINGS   = 5
-
-# 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.
-# The default value is: YES.
-
-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
-# definitions whose arguments contain STL classes (e.g. func(std::string);
-# versus func(std::string) {}). This also make the inheritance and collaboration
-# diagrams that involve STL classes more complete and accurate.
-# The default value is: NO.
-
-BUILTIN_STL_SUPPORT    = NO
-
-# If you use Microsoft's C++/CLI language, you should set this option to YES to
-# enable parsing support.
-# The default value is: NO.
-
-CPP_CLI_SUPPORT        = NO
-
-# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
-# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen
-# will parse them like normal C++ but will assume all classes use public instead
-# of private inheritance when no explicit protection keyword is present.
-# The default value is: 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 will make
-# doxygen to 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.
-# The default value is: YES.
-
-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
-# 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
-# subgrouping. Alternatively, this can be done per class using the
-# \nosubgrouping command.
-# The default value is: YES.
-
-SUBGROUPING            = YES
-
-# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
-# are shown inside the group in which they are included (e.g. using \ingroup)
-# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
-# and RTF).
-#
-# Note that this feature does not work in combination with
-# SEPARATE_MEMBER_PAGES.
-# The default value is: NO.
-
-INLINE_GROUPED_CLASSES = NO
-
-# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
-# with only public data fields or simple typedef fields will be shown inline in
-# the documentation of the scope in which they are defined (i.e. file,
-# namespace, or group documentation), provided this scope is documented. If set
-# to NO, structs, classes, and unions are shown on a separate page (for HTML and
-# Man pages) or section (for LaTeX and RTF).
-# The default value is: NO.
-
-INLINE_SIMPLE_STRUCTS  = NO
-
-# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
-# enum is documented as struct, union, or enum with the name of the typedef. So
-# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
-# with name TypeT. When disabled the typedef will appear as a member of a file,
-# namespace, or class. And the struct will be named TypeS. This can typically be
-# useful for C code in case the coding convention dictates that all compound
-# types are typedef'ed and only the typedef is referenced, never the tag name.
-# The default value is: NO.
-
-TYPEDEF_HIDES_STRUCT   = NO
-
-# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
-# cache is used to resolve symbols given their name and scope. Since this can be
-# an expensive process and often the same symbol appears multiple times in the
-# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
-# doxygen will become slower. If the cache is too large, memory is wasted. The
-# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
-# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
-# symbols. At the end of a run doxygen will report the cache usage and suggest
-# the optimal cache size from a speed point of view.
-# Minimum value: 0, maximum value: 9, default value: 0.
-
-LOOKUP_CACHE_SIZE      = 0
-
-#---------------------------------------------------------------------------
-# Build related configuration options
-#---------------------------------------------------------------------------
-
-# 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.
-# Note: This will also disable the warnings about undocumented members that are
-# normally produced when WARNINGS is set to YES.
-# The default value is: NO.
-
-EXTRACT_ALL            = NO
-
-# 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        = YES
-
-# If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual
-# methods of a class will be included in the documentation.
-# The default value is: NO.
-
-EXTRACT_PRIV_VIRTUAL   = NO
-
-# 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
-# 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,
-# only classes defined in header files are included. Does not have any effect
-# for Java sources.
-# The default value is: YES.
-
-EXTRACT_LOCAL_CLASSES  = YES
-
-# 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.
-# The default value is: NO.
-
-EXTRACT_LOCAL_METHODS  = NO
-
-# If this flag is set to YES, the members of anonymous namespaces will be
-# extracted and appear in the documentation as a namespace called
-# 'anonymous_namespace{file}', where file will be replaced with the base name of
-# the file that contains the anonymous namespace. By default anonymous namespace
-# are hidden.
-# The default value is: NO.
-
-EXTRACT_ANON_NSPACES   = NO
-
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
-# undocumented members inside documented classes or files. If set to NO these
-# members will be included in the various overviews, but no documentation
-# section is generated. This option has no effect if EXTRACT_ALL is enabled.
-# The default value is: NO.
-
-HIDE_UNDOC_MEMBERS     = NO
-
-# 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.
-# The default value is: NO.
-
-HIDE_UNDOC_CLASSES     = NO
-
-# 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.
-# 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
-# blocks will be appended to the function's detailed documentation block.
-# The default value is: NO.
-
-HIDE_IN_BODY_DOCS      = NO
-
-# The INTERNAL_DOCS tag determines if documentation that is typed after a
-# \internal command is included. If the tag is set to NO then the documentation
-# will be excluded. Set it to YES to include the internal documentation.
-# The default value is: 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
-# 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
-# (including Cygwin) ands Mac users are advised to set this option to NO.
-# The default value is: system dependent.
-
-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
-# 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.
-
-SHOW_INCLUDE_FILES     = YES
-
-# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
-# grouped member an include statement to the documentation, telling the reader
-# which file to include in order to use the member.
-# The default value is: NO.
-
-SHOW_GROUPED_MEMB_INC  = NO
-
-# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
-# files with double quotes in the documentation rather than with sharp brackets.
-# The default value is: NO.
-
-FORCE_LOCAL_INCLUDES   = NO
-
-# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
-# documentation for inline members.
-# The default value is: YES.
-
-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.
-# 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
-# this will also influence the order of the classes in the class list.
-# The default value is: NO.
-
-SORT_BRIEF_DOCS        = NO
-
-# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
-# (brief and detailed) documentation of class members so that constructors and
-# destructors are listed first. If set to NO the constructors will appear in the
-# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
-# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
-# member documentation.
-# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
-# detailed member documentation.
-# The default value is: NO.
-
-SORT_MEMBERS_CTORS_1ST = NO
-
-# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
-# of group names into alphabetical order. If set to NO the group names will
-# appear in their defined order.
-# The default value is: NO.
-
-SORT_GROUP_NAMES       = NO
-
-# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
-# fully-qualified names, including namespaces. If set to NO, the class list will
-# be sorted only by class name, not including the namespace part.
-# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
-# Note: This option applies only to the class list, not to the alphabetical
-# list.
-# The default value is: NO.
-
-SORT_BY_SCOPE_NAME     = NO
-
-# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
-# type resolution of all parameters of a function it will reject a match between
-# the prototype and the implementation of a member function even if there is
-# only one candidate or it is obvious which candidate to choose by doing a
-# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
-# accept a match between prototype and implementation in such cases.
-# The default value is: 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 default value is: YES.
-
-GENERATE_TODOLIST      = YES
-
-# 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      = YES
-
-# 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       = YES
-
-# 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.
-
-GENERATE_DEPRECATEDLIST= YES
-
-# The ENABLED_SECTIONS tag can be used to enable conditional documentation
-# sections, marked by \if <section_label> ... \endif and \cond <section_label>
-# ... \endcond blocks.
-
-ENABLED_SECTIONS       =
-
-# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
-# initial value of a variable or macro / define can have for it to appear in the
-# documentation. If the initializer consists of more lines than specified here
-# it will be hidden. Use a value of 0 to hide initializers completely. The
-# appearance of the value of individual variables and macros / defines can be
-# controlled using \showinitializer or \hideinitializer command in the
-# documentation regardless of this setting.
-# Minimum value: 0, maximum value: 10000, default value: 30.
-
-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 default value is: YES.
-
-SHOW_USED_FILES        = YES
-
-# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
-# will remove the Files entry from the Quick Index and from the Folder Tree View
-# (if specified).
-# The default value is: YES.
-
-SHOW_FILES             = YES
-
-# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
-# page. This will remove the Namespaces entry from the Quick Index and from the
-# Folder Tree View (if specified).
-# The default value is: YES.
-
-SHOW_NAMESPACES        = YES
-
-# The FILE_VERSION_FILTER tag can be used to specify a program or script that
-# doxygen should invoke to get the current version for each file (typically from
-# the version control system). Doxygen will invoke the program by executing (via
-# popen()) the command command input-file, where command is the value of the
-# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
-# by doxygen. Whatever the program writes to standard output is used as the file
-# version. For an example see the documentation.
-
-FILE_VERSION_FILTER    =
-
-# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
-# by doxygen. The layout file controls the global structure of the generated
-# output files in an output format independent way. To create the layout file
-# that represents doxygen's defaults, run doxygen with the -l option. You can
-# optionally specify a file name after the option, if omitted DoxygenLayout.xml
-# will be used as the name of the layout file.
-#
-# Note that if you run doxygen from a directory containing a file called
-# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
-# tag is left empty.
-
-LAYOUT_FILE            =
-
-# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
-# the reference definitions. This must be a list of .bib files. The .bib
-# extension is automatically appended if omitted. This requires the bibtex tool
-# to be installed. See also https://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. See also \cite for info how to create references.
-
-CITE_BIB_FILES         =
-
-#---------------------------------------------------------------------------
-# Configuration options related to warning and progress messages
-#---------------------------------------------------------------------------
-
-# The QUIET tag can be used to turn on/off the messages that are generated to
-# standard output by doxygen. If QUIET is set to YES this implies that the
-# messages are off.
-# The default value is: NO.
-
-QUIET                  = NO
-
-# 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
-# this implies that the warnings are on.
-#
-# Tip: Turn warnings on while writing the documentation.
-# The default value is: YES.
-
-WARNINGS               = YES
-
-# 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.
-
-WARN_IF_UNDOCUMENTED   = YES
-
-# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
-# potential errors in the documentation, such as not documenting some parameters
-# in a documented function, or documenting parameters that don't exist or using
-# markup commands wrongly.
-# The default value is: YES.
-
-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. If
-# EXTRACT_ALL is set to YES then this flag will automatically be disabled.
-# 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
-# and the warning text. Optionally the format may contain $version, which will
-# be replaced by the version of the file (if it could be obtained via
-# FILE_VERSION_FILTER)
-# The default value is: $file:$line: $text.
-
-WARN_FORMAT            = "$file:$line: $text"
-
-# The WARN_LOGFILE tag can be used to specify a file to which warning and error
-# messages should be written. If left blank the output is written to standard
-# error (stderr).
-
-WARN_LOGFILE           =
-
-#---------------------------------------------------------------------------
-# Configuration options related to the input files
-#---------------------------------------------------------------------------
-
-# 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. See also FILE_PATTERNS and EXTENSION_MAPPING
-# Note: If this tag is empty the current directory is searched.
-
-INPUT                  = .
-
-# 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
-# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
-# documentation (see: https://www.gnu.org/software/libiconv/) for the list of
-# possible encodings.
-# The default value is: UTF-8.
-
-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.
-#
-# 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 (to be provided as doxygen C comment),
-# *.doc (to be provided as doxygen C comment), *.txt (to be provided as doxygen
-# C comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f, *.for, *.tcl, *.vhd,
-# *.vhdl, *.ucf, *.qsf and *.ice.
-
-FILE_PATTERNS          = *.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 \
-                         *.doc \
-                         *.txt \
-                         *.py \
-                         *.pyw \
-                         *.f90 \
-                         *.f95 \
-                         *.f03 \
-                         *.f08 \
-                         *.f \
-                         *.for \
-                         *.tcl \
-                         *.vhd \
-                         *.vhdl \
-                         *.ucf \
-                         *.qsf \
-                         *.ice
-
-# The RECURSIVE tag can be used to specify whether or not subdirectories should
-# be searched for input files as well.
-# The default value is: NO.
-
-RECURSIVE              = YES
-
-# The EXCLUDE tag can be used to specify files and/or directories that should be
-# excluded from the INPUT source files. This way you can easily exclude a
-# subdirectory from a directory tree whose root is specified with the INPUT tag.
-#
-# Note that relative paths are relative to the directory from which doxygen is
-# run.
-
-EXCLUDE                = build \
-                         cmake-build-debug
-
-# 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
-# from the input.
-# The default value is: NO.
-
-EXCLUDE_SYMLINKS       = NO
-
-# If the value of the INPUT tag contains directories, you can use the
-# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
-# certain files from those directories.
-#
-# 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       =
-
-# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
-# (namespaces, classes, functions, etc.) that should be excluded from the
-# output. The symbol name can be a fully qualified name, a word, or if the
-# wildcard * is used, a substring. Examples: ANamespace, AClass,
-# AClass::ANamespace, ANamespace::*Test
-#
-# Note that the wildcards are matched against the file with absolute path, so to
-# exclude all test directories use the pattern */test/*
-
-EXCLUDE_SYMBOLS        =
-
-# The EXAMPLE_PATH tag can be used to specify one or more files or directories
-# that contain example code fragments that are included (see the \include
-# command).
-
-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       = *
-
-# 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
-# irrespective of the value of the RECURSIVE tag.
-# The default value is: NO.
-
-EXAMPLE_RECURSIVE      = NO
-
-# The IMAGE_PATH tag can be used to specify one or more files or directories
-# that contain images that are to be included in the documentation (see the
-# \image command).
-
-IMAGE_PATH             =
-
-# The INPUT_FILTER tag can be used to specify a program that doxygen should
-# invoke to filter for each input file. Doxygen will invoke the filter program
-# by executing (via popen()) the command:
-#
-# <filter> <input-file>
-#
-# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
-# name of an input file. Doxygen will then use the output that the filter
-# program writes to standard output. If FILTER_PATTERNS is specified, this tag
-# will be ignored.
-#
-# 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           =
-
-# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
-# basis. Doxygen will compare the file name with each pattern and apply the
-# filter if there is a match. The filters are a list of the form: pattern=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
-# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
-# The default value is: NO.
-
-FILTER_SOURCE_FILES    = NO
-
-# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
-# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
-# it is also possible to disable source filtering for a specific pattern using
-# *.ext= (so without naming a filter).
-# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
-
-FILTER_SOURCE_PATTERNS =
-
-# If the USE_MDFILE_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 to reuse the introduction page also for the doxygen output.
-
-USE_MDFILE_AS_MAINPAGE =
-
-#---------------------------------------------------------------------------
-# Configuration options related to source browsing
-#---------------------------------------------------------------------------
-
-# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
-# generated. Documented entities will be cross-referenced with these sources.
-#
-# Note: To get rid of all source code in the generated output, make sure that
-# also VERBATIM_HEADERS is set to NO.
-# The default value is: NO.
-
-SOURCE_BROWSER         = NO
-
-# Setting the INLINE_SOURCES tag to YES will include the body of functions,
-# classes and enums directly into the documentation.
-# The default value is: NO.
-
-INLINE_SOURCES         = NO
-
-# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
-# special comment blocks from generated source code fragments. Normal C, C++ and
-# Fortran comments will always remain visible.
-# The default value is: YES.
-
-STRIP_CODE_COMMENTS    = YES
-
-# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
-# entity all documented functions referencing it will be listed.
-# The default value is: NO.
-
-REFERENCED_BY_RELATION = NO
-
-# If the REFERENCES_RELATION tag is set to YES then for each documented function
-# all documented entities called/used by that function will be listed.
-# The default value is: 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
-# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
-# link to the documentation.
-# The default value is: YES.
-
-REFERENCES_LINK_SOURCE = YES
-
-# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
-# source code will show a tooltip with additional information such as prototype,
-# brief description and links to the definition and documentation. Since this
-# will make the HTML file larger and loading of large files a bit slower, you
-# can opt to disable this feature.
-# The default value is: YES.
-# This tag requires that the tag SOURCE_BROWSER is set to YES.
-
-SOURCE_TOOLTIPS        = YES
-
-# If the USE_HTAGS tag is set to YES then the references to source code will
-# point to the HTML generated by the htags(1) tool instead of doxygen built-in
-# source browser. The htags tool is part of GNU's global source tagging system
-# (see https://www.gnu.org/software/global/global.html). You will need version
-# 4.8.6 or higher.
-#
-# To use it do the following:
-# - Install the latest version of global
-# - Enable SOURCE_BROWSER and USE_HTAGS in the configuration file
-# - Make sure the INPUT points to the root of the source tree
-# - Run doxygen as normal
-#
-# Doxygen will invoke htags (and that will in turn invoke gtags), so these
-# tools must be available from the command line (i.e. in the search path).
-#
-# The result: instead of the source browser generated by doxygen, the links to
-# source code will now point to the output of htags.
-# The default value is: NO.
-# This tag requires that the tag SOURCE_BROWSER is set to YES.
-
-USE_HTAGS              = NO
-
-# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
-# verbatim copy of the header file for each class for which an include is
-# specified. Set to NO to disable this.
-# See also: Section \class.
-# The default value is: YES.
-
-VERBATIM_HEADERS       = YES
-
-# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
-# clang parser (see: http://clang.llvm.org/) for more accurate parsing at the
-# cost of reduced performance. This can be particularly helpful with template
-# rich C++ code for which doxygen's built-in parser lacks the necessary type
-# information.
-# Note: The availability of this option depends on whether or not doxygen was
-# generated with the -Duse_libclang=ON option for CMake.
-# The default value is: NO.
-
-CLANG_ASSISTED_PARSING = NO
-
-# If clang assisted parsing is enabled you can provide the compiler with command
-# line options that you would normally use when invoking the compiler. Note that
-# the include paths will already be set by doxygen for the files and directories
-# specified with INPUT and INCLUDE_PATH.
-# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
-
-CLANG_OPTIONS          =
-
-# If clang assisted parsing is enabled you can provide the clang parser with the
-# path to the compilation database (see:
-# http://clang.llvm.org/docs/HowToSetupToolingForLLVM.html) used when the files
-# were built. This is equivalent to specifying the "-p" option to a clang tool,
-# such as clang-check. These options will then be passed to the parser.
-# Note: The availability of this option depends on whether or not doxygen was
-# generated with the -Duse_libclang=ON option for CMake.
-
-CLANG_DATABASE_PATH    =
-
-#---------------------------------------------------------------------------
-# Configuration options related to the alphabetical class index
-#---------------------------------------------------------------------------
-
-# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
-# compounds will be generated. Enable this if the project contains a lot of
-# classes, structs, unions or interfaces.
-# The default value is: 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
-# while generating the index headers.
-# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
-
-IGNORE_PREFIX          =
-
-#---------------------------------------------------------------------------
-# Configuration options related to the HTML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
-# The default value is: YES.
-
-GENERATE_HTML          = YES
-
-# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
-# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
-# it.
-# The default directory is: html.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_OUTPUT            = html
-
-# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
-# generated HTML page (for example: .htm, .php, .asp).
-# The default value is: .html.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_FILE_EXTENSION    = .html
-
-# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
-# each generated HTML page. If the tag is left blank doxygen will generate a
-# standard header.
-#
-# To get valid HTML the header file that includes any scripts and style sheets
-# that doxygen needs, which is dependent on the configuration options used (e.g.
-# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
-# default header using
-# doxygen -w html new_header.html new_footer.html new_stylesheet.css
-# YourConfigFile
-# and then modify the file new_header.html. See also section "Doxygen usage"
-# for information on how to generate the default header that doxygen normally
-# uses.
-# Note: The header is subject to change so you typically have to regenerate the
-# default header when upgrading to a newer version of doxygen. For a description
-# of the possible markers and block names see the documentation.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_HEADER            =
-
-# 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
-# footer. See HTML_HEADER for more information on how to generate a default
-# footer and what special commands can be used inside the footer. See also
-# section "Doxygen usage" for information on how to generate the default footer
-# that doxygen normally uses.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-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 left blank doxygen will generate a default style sheet.
-# See also section "Doxygen usage" for information on how to generate the style
-# sheet that doxygen normally uses.
-# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
-# it is more robust and this tag (HTML_STYLESHEET) will in the future become
-# obsolete.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_STYLESHEET        =
-
-# 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 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  =
-
-# 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
-# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
-# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
-# files will be copied as-is; there are no commands or markers available.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_EXTRA_FILES       =
-
-# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
-# 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
-# https://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
-# purple, and 360 is red again.
-# Minimum value: 0, maximum value: 359, default value: 220.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_COLORSTYLE_HUE    = 220
-
-# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
-# in the HTML output. For a value of 0 the output will use grayscales only. A
-# value of 255 will produce the most vivid colors.
-# Minimum value: 0, maximum value: 255, default value: 100.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_COLORSTYLE_SAT    = 100
-
-# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
-# luminance component of the colors in the HTML output. Values below 100
-# gradually make the output lighter, whereas values above 100 make the output
-# darker. The value divided by 100 is the actual gamma applied, so 80 represents
-# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
-# change the gamma.
-# Minimum value: 40, maximum value: 240, default value: 80.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-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 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         = NO
-
-# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
-# documentation will contain a main index with vertical navigation menus that
-# are dynamically created via JavaScript. If disabled, the navigation index will
-# consists of multiple levels of tabs that are statically embedded in every HTML
-# page. Disable this option to support browsers that do not have JavaScript,
-# like the Qt help browser.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_DYNAMIC_MENUS     = 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.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_DYNAMIC_SECTIONS  = NO
-
-# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
-# shown in the various tree structured indices initially; the user can expand
-# and collapse entries dynamically later on. Doxygen will expand the tree to
-# such a level that at most the specified number of entries are visible (unless
-# a fully collapsed tree already exceeds this amount). So setting the number of
-# entries 1 will produce a full collapsed tree by default. 0 is a special value
-# representing an infinite number of entries and will result in a full expanded
-# tree by default.
-# Minimum value: 0, maximum value: 9999, default value: 100.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_INDEX_NUM_ENTRIES = 100
-
-# If the GENERATE_DOCSET tag is set to YES, additional index files will be
-# generated that can be used as input for Apple's Xcode 3 integrated development
-# environment (see: https://developer.apple.com/xcode/), introduced with OSX
-# 10.5 (Leopard). To create a documentation set, doxygen will generate a
-# Makefile in the HTML output directory. Running make will produce the docset in
-# that directory and running make install will install the docset in
-# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
-# startup. See https://developer.apple.com/library/archive/featuredarticles/Doxy
-# genXcode/_index.html for more information.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-GENERATE_DOCSET        = NO
-
-# This tag determines the name of the docset feed. A documentation feed provides
-# an umbrella under which multiple documentation sets from a single provider
-# (such as a company or product suite) can be grouped.
-# The default value is: Doxygen generated docs.
-# This tag requires that the tag GENERATE_DOCSET is set to YES.
-
-DOCSET_FEEDNAME        = "Doxygen generated docs"
-
-# This tag specifies a string that should uniquely identify the documentation
-# set bundle. This should be a reverse domain-name style string, e.g.
-# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
-# The default value is: org.doxygen.Project.
-# This tag requires that the tag GENERATE_DOCSET is set to YES.
-
-DOCSET_BUNDLE_ID       = org.doxygen.Project
-
-# The DOCSET_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.
-# The default value is: org.doxygen.Publisher.
-# This tag requires that the tag GENERATE_DOCSET is set to YES.
-
-DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
-
-# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
-# The default value is: Publisher.
-# This tag requires that the tag GENERATE_DOCSET is set to YES.
-
-DOCSET_PUBLISHER_NAME  = Publisher
-
-# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
-# 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
-# (see: https://www.microsoft.com/en-us/download/details.aspx?id=21138) on
-# Windows.
-#
-# The HTML Help Workshop contains a compiler that can convert all HTML output
-# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
-# files are now used as the Windows 98 help format, and will replace the old
-# Windows help format (.hlp) on all Windows platforms in the future. Compressed
-# HTML files also contain an index, a table of contents, and you can search for
-# words in the documentation. The HTML workshop also contains a viewer for
-# compressed HTML files.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-GENERATE_HTMLHELP      = NO
-
-# The CHM_FILE tag can be used to specify the file name of the resulting .chm
-# file. You can add a path in front of the file if the result should not be
-# written to the html output directory.
-# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
-
-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,
-# 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 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)
-# 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. 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.
-
-BINARY_TOC             = NO
-
-# The TOC_EXPAND flag can be set to YES to add extra items for group members to
-# the table of contents of the HTML help documentation and to the tree view.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
-
-TOC_EXPAND             = NO
-
-# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
-# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
-# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
-# (.qch) of the generated HTML documentation.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-GENERATE_QHP           = NO
-
-# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
-# the file name of the resulting .qch file. The path specified is relative to
-# the HTML output folder.
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QCH_FILE               =
-
-# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
-# Project output. For more information please see Qt Help Project / Namespace
-# (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace).
-# The default value is: org.doxygen.Project.
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHP_NAMESPACE          = org.doxygen.Project
-
-# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
-# Help Project output. For more information please see Qt Help Project / Virtual
-# Folders (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual-
-# folders).
-# The default value is: doc.
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHP_VIRTUAL_FOLDER     = doc
-
-# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
-# filter to add. For more information please see Qt Help Project / Custom
-# Filters (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-
-# filters).
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHP_CUST_FILTER_NAME   =
-
-# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
-# custom filter to add. For more information please see Qt Help Project / Custom
-# Filters (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-
-# filters).
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHP_CUST_FILTER_ATTRS  =
-
-# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
-# project's filter section matches. Qt Help Project / Filter Attributes (see:
-# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#filter-attributes).
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHP_SECT_FILTER_ATTRS  =
-
-# The QHG_LOCATION tag can be used to specify the location of Qt's
-# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the
-# generated .qhp file.
-# This tag requires that the tag GENERATE_QHP is set to YES.
-
-QHG_LOCATION           =
-
-# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
-# generated, together with the HTML files, they form an Eclipse help plugin. To
-# install this plugin and make it available under the help contents menu in
-# Eclipse, the contents of the directory containing the HTML and XML files needs
-# to be copied into the plugins directory of eclipse. The name of the directory
-# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
-# After copying Eclipse needs to be restarted before the help appears.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-GENERATE_ECLIPSEHELP   = NO
-
-# A unique identifier for the Eclipse help plugin. When installing the plugin
-# the directory name containing the HTML and XML files should also have this
-# name. Each documentation set should have its own identifier.
-# The default value is: org.doxygen.Project.
-# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
-
-ECLIPSE_DOC_ID         = org.doxygen.Project
-
-# If you want full control over the layout of the generated HTML pages it might
-# be necessary to disable the index and replace it with your own. The
-# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
-# 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.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-DISABLE_INDEX          = NO
-
-# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
-# structure should be generated to display hierarchical information. If the tag
-# value is set to YES, a side panel will be generated containing a tree-like
-# 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 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
-# the same information as the tab index, you could consider setting
-# DISABLE_INDEX to YES when enabling this option.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-GENERATE_TREEVIEW      = YES
-
-# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
-# doxygen will group on one line in the generated HTML documentation.
-#
-# Note that a value of 0 will completely suppress the enum values from appearing
-# in the overview section.
-# Minimum value: 0, maximum value: 20, default value: 4.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-ENUM_VALUES_PER_LINE   = 4
-
-# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
-# to set the initial width (in pixels) of the frame in which the tree is shown.
-# Minimum value: 0, maximum value: 1500, default value: 250.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-TREEVIEW_WIDTH         = 250
-
-# 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.
-
-EXT_LINKS_IN_WINDOW    = NO
-
-# Use this tag to change the font size of LaTeX formulas included as images in
-# the HTML documentation. When you change the font size after a successful
-# doxygen run you need to manually remove any form_*.png images from the HTML
-# output directory to force them to be regenerated.
-# Minimum value: 8, maximum value: 50, default value: 10.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-FORMULA_FONTSIZE       = 10
-
-# Use the FORMULA_TRANSPARENT 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
-
-# The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands
-# to create new LaTeX commands to be used in formulas as building blocks. See
-# the section "Including formulas" for details.
-
-FORMULA_MACROFILE      =
-
-# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
-# https://www.mathjax.org) which uses client side JavaScript for the rendering
-# 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.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-USE_MATHJAX            = NO
-
-# 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.
-# Possible values are: HTML-CSS (which is slower, but has the best
-# compatibility), NativeMML (i.e. MathML) and SVG.
-# The default value is: HTML-CSS.
-# This tag requires that the tag USE_MATHJAX is set to YES.
-
-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 directory
-# is located at the same level as the HTML output directory, then
-# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
-# Content Delivery Network so you can quickly see the result without installing
-# MathJax. However, it is strongly recommended to install a local copy of
-# MathJax from https://www.mathjax.org before deployment.
-# The default value is: https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/.
-# This tag requires that the tag USE_MATHJAX is set to YES.
-
-MATHJAX_RELPATH        = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/
-
-# 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     =
-
-# 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
-# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an
-# example see the documentation.
-# This tag requires that the tag USE_MATHJAX is set to YES.
-
-MATHJAX_CODEFILE       =
-
-# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
-# the HTML output. The underlying search engine uses javascript and DHTML and
-# should work on any modern browser. Note that when using HTML help
-# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
-# there is already a search function so this one should typically be disabled.
-# For large projects the javascript based search engine can be slow, then
-# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
-# search using the keyboard; to jump to the search box use <access key> + S
-# (what the <access key> is depends on the OS and browser, but it is typically
-# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
-# key> to jump into the search results window, the results can be navigated
-# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
-# the search. The filter options can be selected when the cursor is inside the
-# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
-# to select a filter and <Enter> or <escape> to activate or cancel the filter
-# option.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-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 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.
-
-SERVER_BASED_SEARCH    = NO
-
-# When EXTERNAL_SEARCH tag 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: https://xapian.org/).
-#
-# 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.
-
-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
-# (doxysearch.cgi) which are based on the open source search engine library
-# Xapian (see: https://xapian.org/). See the section "External Indexing and
-# Searching" for details.
-# This tag requires that the tag SEARCHENGINE is set to YES.
-
-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.
-# The default file is: searchdata.xml.
-# This tag requires that the tag SEARCHENGINE is set to YES.
-
-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.
-# This tag requires that the tag SEARCHENGINE is set to YES.
-
-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 = tagname1=loc1 tagname2=loc2 ...
-# This tag requires that the tag SEARCHENGINE is set to YES.
-
-EXTRA_SEARCH_MAPPINGS  =
-
-#---------------------------------------------------------------------------
-# Configuration options related to the LaTeX output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
-# The default value is: YES.
-
-GENERATE_LATEX         = YES
-
-# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
-# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
-# it.
-# The default directory is: latex.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_OUTPUT           = latex
-
-# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
-# invoked.
-#
-# Note that when not enabling USE_PDFLATEX the default is latex when enabling
-# USE_PDFLATEX the default is pdflatex and when in the later case latex is
-# chosen this is overwritten by pdflatex. For specific output languages the
-# default can have been set differently, this depends on the implementation of
-# the output language.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_CMD_NAME         =
-
-# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
-# index for LaTeX.
-# Note: This tag is used in the Makefile / make.bat.
-# See also: LATEX_MAKEINDEX_CMD for the part in the generated output file
-# (.tex).
-# The default file is: makeindex.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-MAKEINDEX_CMD_NAME     = makeindex
-
-# The LATEX_MAKEINDEX_CMD tag can be used to specify the command name to
-# generate index for LaTeX. In case there is no backslash (\) as first character
-# it will be automatically added in the LaTeX code.
-# Note: This tag is used in the generated output file (.tex).
-# See also: MAKEINDEX_CMD_NAME for the part in the Makefile / make.bat.
-# The default value is: makeindex.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_MAKEINDEX_CMD    = makeindex
-
-# 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.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-COMPACT_LATEX          = NO
-
-# The PAPER_TYPE tag can be used to set the paper type that is used by the
-# printer.
-# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
-# 14 inches) and executive (7.25 x 10.5 inches).
-# The default value is: a4.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-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. 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         =
-
-# 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
-# chapter. If it is left blank doxygen will generate a standard header. See
-# section "Doxygen usage" for information on how to let doxygen write the
-# default header to a separate file.
-#
-# 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,
-# $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. 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
-# markers available.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_EXTRA_FILES      =
-
-# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
-# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
-# contain links (just like the HTML output) instead of page references. This
-# makes the output suitable for online browsing using a PDF viewer.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-PDF_HYPERLINKS         = YES
-
-# 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.
-
-USE_PDFLATEX           = YES
-
-# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
-# command to the generated LaTeX files. This will instruct LaTeX to keep running
-# if errors occur, instead of asking the user for help. This option is also used
-# when generating formulas in HTML.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_BATCHMODE        = NO
-
-# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
-# index chapters (such as File Index, Compound Index, etc.) in the output.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-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
-# https://en.wikipedia.org/wiki/BibTeX and \cite for more info.
-# The default value is: plain.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-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
-
-# 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,
-# it will be relative to the LATEX_OUTPUT directory. If left blank the
-# LATEX_OUTPUT directory will be used.
-# This tag requires that the tag GENERATE_LATEX is set to YES.
-
-LATEX_EMOJI_DIRECTORY  =
-
-#---------------------------------------------------------------------------
-# Configuration options related to the RTF output
-#---------------------------------------------------------------------------
-
-# 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.
-
-GENERATE_RTF           = NO
-
-# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
-# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
-# it.
-# The default directory is: rtf.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_OUTPUT             = 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.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-COMPACT_RTF            = NO
-
-# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
-# contain hyperlink fields. The RTF file will contain links (just like the HTML
-# output) instead of page references. This makes the output suitable for online
-# browsing using Word or some other Word compatible readers that support those
-# fields.
-#
-# Note: WordPad (write) and others do not support links.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_HYPERLINKS         = NO
-
-# Load stylesheet definitions from file. Syntax is similar to doxygen's
-# configuration file, i.e. a series of assignments. You only have to provide
-# replacements, missing definitions are set to their default value.
-#
-# See also section "Doxygen usage" for information on how to generate the
-# default style sheet that doxygen normally uses.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_STYLESHEET_FILE    =
-
-# Set optional variables used in the generation of an RTF document. Syntax is
-# similar to doxygen's configuration file. A template extensions file can be
-# generated using doxygen -e rtf extensionFile.
-# This tag requires that the tag GENERATE_RTF is set to YES.
-
-RTF_EXTENSIONS_FILE    =
-
-# If the RTF_SOURCE_CODE tag is set to YES then doxygen will include source code
-# with syntax highlighting in the RTF 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_RTF is set to YES.
-
-RTF_SOURCE_CODE        = NO
-
-#---------------------------------------------------------------------------
-# Configuration options related to the man page output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
-# classes and files.
-# The default value is: NO.
-
-GENERATE_MAN           = NO
-
-# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
-# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
-# it. A directory man3 will be created inside the directory specified by
-# MAN_OUTPUT.
-# The default directory is: man.
-# This tag requires that the tag GENERATE_MAN is set to YES.
-
-MAN_OUTPUT             = man
-
-# The MAN_EXTENSION tag determines the extension that is added to the generated
-# man pages. In case the manual section does not start with a number, the number
-# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
-# optional.
-# The default value is: .3.
-# This tag requires that the tag GENERATE_MAN is set to YES.
-
-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
-# them the man command would be unable to find the correct page.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_MAN is set to YES.
-
-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
-# captures the structure of the code including all documentation.
-# The default value is: NO.
-
-GENERATE_XML           = NO
-
-# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
-# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
-# it.
-# The default directory is: xml.
-# This tag requires that the tag GENERATE_XML is set to YES.
-
-XML_OUTPUT             = xml
-
-# 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.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_XML is set to YES.
-
-XML_PROGRAMLISTING     = YES
-
-# If the XML_NS_MEMB_FILE_SCOPE tag is set to YES, doxygen will include
-# namespace members in file scope as well, matching the HTML output.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_XML is set to YES.
-
-XML_NS_MEMB_FILE_SCOPE = NO
-
-#---------------------------------------------------------------------------
-# Configuration options related to the DOCBOOK output
-#---------------------------------------------------------------------------
-
-# 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.
-
-GENERATE_DOCBOOK       = NO
-
-# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
-# front of it.
-# The default directory is: docbook.
-# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
-
-DOCBOOK_OUTPUT         = docbook
-
-# If the DOCBOOK_PROGRAMLISTING tag is set to YES, doxygen will include the
-# program listings (including syntax highlighting and cross-referencing
-# information) to the DOCBOOK output. Note that enabling this will significantly
-# increase the size of the DOCBOOK output.
-# The default value is: NO.
-# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
-
-DOCBOOK_PROGRAMLISTING = NO
-
-#---------------------------------------------------------------------------
-# 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.sourceforge.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
-
-#---------------------------------------------------------------------------
-# Configuration options related to the Perl module output
-#---------------------------------------------------------------------------
-
-# 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.
-# The default value is: NO.
-
-GENERATE_PERLMOD       = NO
-
-# 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.
-# This tag requires that the tag GENERATE_PERLMOD is set to YES.
-
-PERLMOD_LATEX          = NO
-
-# 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
-# size of the Perl module output will be much smaller and Perl will parse it
-# just the same.
-# The default value is: YES.
-# This tag requires that the tag GENERATE_PERLMOD is set to YES.
-
-PERLMOD_PRETTY         = YES
-
-# The names of the make variables in the generated doxyrules.make file are
-# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
-# so different doxyrules.make files included by the same Makefile don't
-# overwrite each other's variables.
-# This tag requires that the tag GENERATE_PERLMOD is set to YES.
-
-PERLMOD_MAKEVAR_PREFIX =
-
-#---------------------------------------------------------------------------
-# Configuration options related to the preprocessor
-#---------------------------------------------------------------------------
-
-# 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
-# performed. Macro expansion can be done in a controlled way by setting
-# EXPAND_ONLY_PREDEF to YES.
-# The default value is: NO.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-MACRO_EXPANSION        = NO
-
-# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
-# the macro expansion is limited to the macros specified with the PREDEFINED and
-# EXPAND_AS_DEFINED tags.
-# The default value is: NO.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-EXPAND_ONLY_PREDEF     = NO
-
-# 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.
-
-SEARCH_INCLUDES        = YES
-
-# The INCLUDE_PATH tag can be used to specify one or more directories that
-# contain include files that are not input files but should be processed by the
-# preprocessor.
-# This tag requires that the tag SEARCH_INCLUDES is set to YES.
-
-INCLUDE_PATH           =
-
-# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
-# patterns (like *.h and *.hpp) to filter out the header-files in the
-# directories. If left blank, the patterns specified with FILE_PATTERNS will be
-# used.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-INCLUDE_FILE_PATTERNS  =
-
-# The PREDEFINED tag can be used to specify one or more macro names that are
-# defined before the preprocessor is started (similar to the -D option of e.g.
-# gcc). The argument of the tag is a list of macros of the form: name or
-# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
-# is assumed. To prevent a macro definition from being undefined via #undef or
-# recursively expanded use the := operator instead of the = operator.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-PREDEFINED             =
-
-# 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. The
-# macro definition that is found in the sources will be used. Use the PREDEFINED
-# tag if you want to use a different macro definition that overrules the
-# definition found in the source code.
-# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
-
-EXPAND_AS_DEFINED      =
-
-# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
-# 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.
-
-SKIP_FUNCTION_MACROS   = YES
-
-#---------------------------------------------------------------------------
-# Configuration options related to external references
-#---------------------------------------------------------------------------
-
-# The TAGFILES tag can be used to specify one or more tag files. For each tag
-# file the location of the external documentation should be added. The format of
-# a tag file without this location is as follows:
-# TAGFILES = file1 file2 ...
-# Adding location for the tag files is done as follows:
-# TAGFILES = file1=loc1 "file2 = loc2" ...
-# 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 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.
-
-TAGFILES               =
-
-# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
-# tag file that is based on the input files it reads. See section "Linking to
-# external documentation" for more information about the usage of tag files.
-
-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.
-# 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
-# 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
-# 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
-
-#---------------------------------------------------------------------------
-# 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         = YES
-
-# 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
-# DIA_PATH tag allows you to specify the directory where the dia binary resides.
-# If left empty dia is assumed to be found in the default search path.
-
-DIA_PATH               =
-
-# 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.
-
-HIDE_UNDOC_RELATIONS   = YES
-
-# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
-# available from the path. This tool is part of Graphviz (see:
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-<div class="line">    │   └── lib</div>
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-\chapter{Context\+SV Outline}
-\hypertarget{md_doc_2_o_u_t_l_i_n_e}{}\label{md_doc_2_o_u_t_l_i_n_e}\index{ContextSV Outline@{ContextSV Outline}}
-\label{md_doc_2_o_u_t_l_i_n_e_autotoc_md0}%
-\Hypertarget{md_doc_2_o_u_t_l_i_n_e_autotoc_md0}%
- \hypertarget{md_doc_2_o_u_t_l_i_n_e_autotoc_md1}{}\doxysection{\texorpdfstring{External dependencies}{External dependencies}}\label{md_doc_2_o_u_t_l_i_n_e_autotoc_md1}
-\tabulinesep=1mm
-\begin{longtabu}spread 0pt [c]{*{3}{|X[-1]}|}
-\hline
-\PBS\centering \cellcolor{\tableheadbgcolor}\textbf{ Dependency   }&\PBS\centering \cellcolor{\tableheadbgcolor}\textbf{ Use   }&\PBS\centering \cellcolor{\tableheadbgcolor}\textbf{ Installation    }\\\cline{1-3}
-\endfirsthead
-\hline
-\endfoot
-\hline
-\PBS\centering \cellcolor{\tableheadbgcolor}\textbf{ Dependency   }&\PBS\centering \cellcolor{\tableheadbgcolor}\textbf{ Use   }&\PBS\centering \cellcolor{\tableheadbgcolor}\textbf{ Installation    }\\\cline{1-3}
-\endhead
-HTSLib   &Reading BAM files.   &\href{https://www.biostars.org/p/328831/}{\texttt{ https\+://www.\+biostars.\+org/p/328831/}} ~\newline
- \href{http://www.htslib.org/download/}{\texttt{ http\+://www.\+htslib.\+org/download/}}    \\\cline{1-3}
-Tensorflow   &Importing the SV scoring model.   &\href{https://www.tensorflow.org/install/lang_c}{\texttt{ https\+://www.\+tensorflow.\+org/install/lang\+\_\+c}}   \\\cline{1-3}
-\end{longtabu}
-\hypertarget{md_doc_2_o_u_t_l_i_n_e_autotoc_md2}{}\doxysection{\texorpdfstring{SV scoring model}{SV scoring model}}\label{md_doc_2_o_u_t_l_i_n_e_autotoc_md2}
-The SV scoring model is trained and saved as a Tensorflow weighted graph in PB file format. It can be trained via the \href{https://www.tensorflow.org/api_docs/python/tf}{\texttt{ Python API}}. The \href{https://www.tensorflow.org/api_docs/cc}{\texttt{ C++ API}} is used to import and utilize this model for scoring SVs.\hypertarget{md_doc_2_o_u_t_l_i_n_e_autotoc_md3}{}\doxysubsection{\texorpdfstring{Training the model}{Training the model}}\label{md_doc_2_o_u_t_l_i_n_e_autotoc_md3}
-\hypertarget{md_doc_2_o_u_t_l_i_n_e_autotoc_md4}{}\doxysection{\texorpdfstring{Project structure}{Project structure}}\label{md_doc_2_o_u_t_l_i_n_e_autotoc_md4}
-
-\begin{DoxyCode}{0}
-\DoxyCodeLine{ContextSV}
-\DoxyCodeLine{├──\ include}
-\DoxyCodeLine{│\ \ \ └──\ ContextSV.h}
-\DoxyCodeLine{├──\ src}
-\DoxyCodeLine{│\ \ \ └──\ ContextSV.cpp}
-\DoxyCodeLine{└──\ tests}
-\DoxyCodeLine{│\ \ \ ├──\ BasicTests.cpp}
-\DoxyCodeLine{│\ \ \ ├──\ AccuracyTests.cpp}
-\DoxyCodeLine{│\ \ \ └──\ ScoringModelTests.cpp}
-\DoxyCodeLine{└──\ lib}
-\DoxyCodeLine{\ \ \ \ ├──\ tensorflow}
-\DoxyCodeLine{\ \ \ \ |\ \ \ ├──\ LICENSE}
-\DoxyCodeLine{\ \ \ \ │\ \ \ ├──\ include}
-\DoxyCodeLine{\ \ \ \ │\ \ \ │\ \ \ └──\ ...}
-\DoxyCodeLine{\ \ \ \ │\ \ \ └──\ lib}
-\DoxyCodeLine{\ \ \ \ │\ \ \ \ \ \ \ └──\ ...}
-\DoxyCodeLine{\ \ \ \ └──\ htslib}
-\DoxyCodeLine{\ \ \ \ \ \ \ \ ├──\ LICENSE}
-\DoxyCodeLine{\ \ \ \ \ \ \ \ ├──\ include}
-\DoxyCodeLine{\ \ \ \ \ \ \ \ │\ \ \ └──\ ...}
-\DoxyCodeLine{\ \ \ \ \ \ \ \ └──\ lib}
-\DoxyCodeLine{\ \ \ \ \ \ \ \ \ \ \ \ └──\ ...}
-
-\end{DoxyCode}
-\hypertarget{md_doc_2_o_u_t_l_i_n_e_autotoc_md5}{}\doxysection{\texorpdfstring{Tasks by order}{Tasks by order}}\label{md_doc_2_o_u_t_l_i_n_e_autotoc_md5}
-
-\begin{DoxyItemize}
-\item \mbox{[}x\mbox{]} Draft project structure
-\item \mbox{[} \mbox{]} CLI with BAM file input 
-\end{DoxyItemize}
\ No newline at end of file
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diff --git a/docs/doxygen/latex/project-outline_8md.tex b/docs/doxygen/latex/project-outline_8md.tex
deleted file mode 100644
index 36fc3ea7..00000000
--- a/docs/doxygen/latex/project-outline_8md.tex
+++ /dev/null
@@ -1,2 +0,0 @@
-\doxysection{doc/project-\/outline.md File Reference}
-\hypertarget{project-outline_8md}{}\label{project-outline_8md}\index{doc/project-\/outline.md@{doc/project-\/outline.md}}
diff --git a/docs/doxygen/latex/struct_region_coverage.tex b/docs/doxygen/latex/struct_region_coverage.tex
deleted file mode 100644
index 8e5180fd..00000000
--- a/docs/doxygen/latex/struct_region_coverage.tex
+++ /dev/null
@@ -1,22 +0,0 @@
-\doxysection{Region\+Coverage Struct Reference}
-\hypertarget{struct_region_coverage}{}\label{struct_region_coverage}\index{RegionCoverage@{RegionCoverage}}
-\doxysubsubsection*{Public Attributes}
-\begin{DoxyCompactItemize}
-\item 
-\Hypertarget{struct_region_coverage_aeaf05c26f621e236e38dd0393fa32b82}\label{struct_region_coverage_aeaf05c26f621e236e38dd0393fa32b82} 
-bool {\bfseries valid} = false
-\item 
-\Hypertarget{struct_region_coverage_a8ff3c57058d1523ab487cf7261ea0505}\label{struct_region_coverage_a8ff3c57058d1523ab487cf7261ea0505} 
-uint64\+\_\+t {\bfseries length} = 0
-\item 
-\Hypertarget{struct_region_coverage_aece2e3d4f6a4e2a3a3e8c799bb0414ca}\label{struct_region_coverage_aece2e3d4f6a4e2a3a3e8c799bb0414ca} 
-double {\bfseries mean} = 0
-\item 
-\Hypertarget{struct_region_coverage_a859bbec766be8b90f778119558ee847c}\label{struct_region_coverage_a859bbec766be8b90f778119558ee847c} 
-double {\bfseries baf} = 0
-\end{DoxyCompactItemize}
-
-
-The documentation for this struct was generated from the following file\+:\begin{DoxyCompactItemize}
-\item 
-include/cnv\+\_\+caller.\+h\end{DoxyCompactItemize}
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diff --git a/docs/doxygen/latex/md__r_e_a_d_m_e.tex b/latex/md__r_e_a_d_m_e.tex
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diff --git a/docs/doxygen/latex/md_doc_2genome-assembly-guide.tex b/latex/md_docs_2genome-assembly-guide.tex
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index f4384998..fe3ec1e0 100644
--- a/docs/doxygen/latex/md_doc_2genome-assembly-guide.tex
+++ b/latex/md_docs_2genome-assembly-guide.tex
@@ -1,38 +1,38 @@
 \chapter{Hybrid Optical Map-\/\+Guided Assembly}
-\hypertarget{md_doc_2genome-assembly-guide}{}\label{md_doc_2genome-assembly-guide}\index{Hybrid Optical Map-\/Guided Assembly@{Hybrid Optical Map-\/Guided Assembly}}
-\label{md_doc_2genome-assembly-guide_autotoc_md0}%
-\Hypertarget{md_doc_2genome-assembly-guide_autotoc_md0}%
- \hypertarget{md_doc_2genome-assembly-guide_autotoc_md1}{}\doxysection{\texorpdfstring{Download Test Data}{Download Test Data}}\label{md_doc_2genome-assembly-guide_autotoc_md1}
+\hypertarget{md_docs_2genome-assembly-guide}{}\label{md_docs_2genome-assembly-guide}\index{Hybrid Optical Map-\/Guided Assembly@{Hybrid Optical Map-\/Guided Assembly}}
+\label{md_docs_2genome-assembly-guide_autotoc_md0}%
+\Hypertarget{md_docs_2genome-assembly-guide_autotoc_md0}%
+ \hypertarget{md_docs_2genome-assembly-guide_autotoc_md1}{}\doxysection{\texorpdfstring{Download Test Data}{Download Test Data}}\label{md_docs_2genome-assembly-guide_autotoc_md1}
 Input data is from GIAB\+: Oxford Nanopore ultralong (guppy-\/\+V3.\+2.\+4\+\_\+2020-\/01-\/22)
 
-\href{https://github.com/genome-in-a-bottle/giab_data_indexes}{\texttt{ https\+://github.\+com/genome-\/in-\/a-\/bottle/giab\+\_\+data\+\_\+indexes}}\hypertarget{md_doc_2genome-assembly-guide_autotoc_md2}{}\doxysection{\texorpdfstring{De novo Assembly}{De novo Assembly}}\label{md_doc_2genome-assembly-guide_autotoc_md2}
+\href{https://github.com/genome-in-a-bottle/giab_data_indexes}{\texttt{ https\+://github.\+com/genome-\/in-\/a-\/bottle/giab\+\_\+data\+\_\+indexes}}\hypertarget{md_docs_2genome-assembly-guide_autotoc_md2}{}\doxysection{\texorpdfstring{De novo Assembly}{De novo Assembly}}\label{md_docs_2genome-assembly-guide_autotoc_md2}
 We will perform de novo assembly of the hg002 data using miniasm (instructions from \href{https://github.com/lh3/miniasm}{\texttt{ https\+://github.\+com/lh3/miniasm}})
 
 
 \begin{DoxyItemize}
 \item Also see Optical Kermit\textquotesingle{}s optical map guided assembly script, which uses the same tools and approach (\href{https://github.com/Denopia/kermit-optical-maps/blob/master/genome-assembly.sh}{\texttt{ https\+://github.\+com/\+Denopia/kermit-\/optical-\/maps/blob/master/genome-\/assembly.\+sh}})
-\end{DoxyItemize}\hypertarget{md_doc_2genome-assembly-guide_autotoc_md3}{}\doxysubsection{\texorpdfstring{Set up the software environment\+:}{Set up the software environment:}}\label{md_doc_2genome-assembly-guide_autotoc_md3}
+\end{DoxyItemize}\hypertarget{md_docs_2genome-assembly-guide_autotoc_md3}{}\doxysubsection{\texorpdfstring{Set up the software environment\+:}{Set up the software environment:}}\label{md_docs_2genome-assembly-guide_autotoc_md3}
 
 \begin{DoxyCode}{0}
 \DoxyCodeLine{export\ PATH="{}\$software\_dir"{}/minimap2:\$PATH}
 \DoxyCodeLine{export\ PATH="{}\$software\_dir"{}/miniasm:\$PATH}
 
 \end{DoxyCode}
-\hypertarget{md_doc_2genome-assembly-guide_autotoc_md4}{}\doxysubsection{\texorpdfstring{Use minimap2 to self-\/align the hg002 data\+:}{Use minimap2 to self-align the hg002 data:}}\label{md_doc_2genome-assembly-guide_autotoc_md4}
+\hypertarget{md_docs_2genome-assembly-guide_autotoc_md4}{}\doxysubsection{\texorpdfstring{Use minimap2 to self-\/align the hg002 data\+:}{Use minimap2 to self-align the hg002 data:}}\label{md_docs_2genome-assembly-guide_autotoc_md4}
 
 \begin{DoxyCode}{0}
 \DoxyCodeLine{\ "{}Running\ minimap2..."{}}
 \DoxyCodeLine{minimap2\ -\/x\ ava-\/ont\ -\/t\ 12\ input\_data/HG002\_hs37d5\_ONT\_GIAB.fastq\ input\_data/HG002\_hs37d5\_ONT\_GIAB.fastq\ |\ gzip\ -\/1\ >\ output/HG002\_hs37d5\_ONT\_GIAB.paf.gz}
 
 \end{DoxyCode}
-\hypertarget{md_doc_2genome-assembly-guide_autotoc_md5}{}\doxysubsection{\texorpdfstring{Use miniasm to assemble the self-\/aligned data\+:}{Use miniasm to assemble the self-aligned data:}}\label{md_doc_2genome-assembly-guide_autotoc_md5}
+\hypertarget{md_docs_2genome-assembly-guide_autotoc_md5}{}\doxysubsection{\texorpdfstring{Use miniasm to assemble the self-\/aligned data\+:}{Use miniasm to assemble the self-aligned data:}}\label{md_docs_2genome-assembly-guide_autotoc_md5}
 
 \begin{DoxyCode}{0}
 \DoxyCodeLine{echo\ "{}Running\ miniasm..."{}}
 \DoxyCodeLine{miniasm\ -\/f\ inputs/HG002\_hs37d5\_ONT\_GIAB.fastq\ outputs/HG002\_hs37d5\_ONT\_GIAB.paf.gz\ >\ outputs/HG002\_hs37d5\_ONT\_GIAB.gfa}
 
 \end{DoxyCode}
-\hypertarget{md_doc_2genome-assembly-guide_autotoc_md6}{}\doxysubsection{\texorpdfstring{Convert GFA file to FASTA for downstream analysis}{Convert GFA file to FASTA for downstream analysis}}\label{md_doc_2genome-assembly-guide_autotoc_md6}
+\hypertarget{md_docs_2genome-assembly-guide_autotoc_md6}{}\doxysubsection{\texorpdfstring{Convert GFA file to FASTA for downstream analysis}{Convert GFA file to FASTA for downstream analysis}}\label{md_docs_2genome-assembly-guide_autotoc_md6}
 (instructions from \href{https://www.biostars.org/p/169516/}{\texttt{ https\+://www.\+biostars.\+org/p/169516/}})
 
 
diff --git a/docs/doxygen/latex/md_doc_2project-outline.tex b/latex/md_docs_2project-outline.tex
similarity index 70%
rename from docs/doxygen/latex/md_doc_2project-outline.tex
rename to latex/md_docs_2project-outline.tex
index 6f20e54e..e5e8667a 100644
--- a/docs/doxygen/latex/md_doc_2project-outline.tex
+++ b/latex/md_docs_2project-outline.tex
@@ -1,8 +1,8 @@
 \chapter{Context\+SV Outline}
-\hypertarget{md_doc_2project-outline}{}\label{md_doc_2project-outline}\index{ContextSV Outline@{ContextSV Outline}}
-\label{md_doc_2project-outline_autotoc_md7}%
-\Hypertarget{md_doc_2project-outline_autotoc_md7}%
- \hypertarget{md_doc_2project-outline_autotoc_md8}{}\doxysection{\texorpdfstring{External dependencies}{External dependencies}}\label{md_doc_2project-outline_autotoc_md8}
+\hypertarget{md_docs_2project-outline}{}\label{md_docs_2project-outline}\index{ContextSV Outline@{ContextSV Outline}}
+\label{md_docs_2project-outline_autotoc_md7}%
+\Hypertarget{md_docs_2project-outline_autotoc_md7}%
+ \hypertarget{md_docs_2project-outline_autotoc_md8}{}\doxysection{\texorpdfstring{External dependencies}{External dependencies}}\label{md_docs_2project-outline_autotoc_md8}
 \tabulinesep=1mm
 \begin{longtabu}spread 0pt [c]{*{3}{|X[-1]}|}
 \hline
@@ -17,9 +17,9 @@ \chapter{Context\+SV Outline}
  \href{http://www.htslib.org/download/}{\texttt{ http\+://www.\+htslib.\+org/download/}}    \\\cline{1-3}
 Tensorflow   &Importing the SV scoring model.   &\href{https://www.tensorflow.org/install/lang_c}{\texttt{ https\+://www.\+tensorflow.\+org/install/lang\+\_\+c}}   \\\cline{1-3}
 \end{longtabu}
-\hypertarget{md_doc_2project-outline_autotoc_md9}{}\doxysection{\texorpdfstring{SV scoring model}{SV scoring model}}\label{md_doc_2project-outline_autotoc_md9}
-The SV scoring model is trained and saved as a Tensorflow weighted graph in PB file format. It can be trained via the \href{https://www.tensorflow.org/api_docs/python/tf}{\texttt{ Python API}}. The \href{https://www.tensorflow.org/api_docs/cc}{\texttt{ C++ API}} is used to import and utilize this model for scoring SVs.\hypertarget{md_doc_2project-outline_autotoc_md10}{}\doxysubsection{\texorpdfstring{Training the model}{Training the model}}\label{md_doc_2project-outline_autotoc_md10}
-\hypertarget{md_doc_2project-outline_autotoc_md11}{}\doxysection{\texorpdfstring{Project structure}{Project structure}}\label{md_doc_2project-outline_autotoc_md11}
+\hypertarget{md_docs_2project-outline_autotoc_md9}{}\doxysection{\texorpdfstring{SV scoring model}{SV scoring model}}\label{md_docs_2project-outline_autotoc_md9}
+The SV scoring model is trained and saved as a Tensorflow weighted graph in PB file format. It can be trained via the \href{https://www.tensorflow.org/api_docs/python/tf}{\texttt{ Python API}}. The \href{https://www.tensorflow.org/api_docs/cc}{\texttt{ C++ API}} is used to import and utilize this model for scoring SVs.\hypertarget{md_docs_2project-outline_autotoc_md10}{}\doxysubsection{\texorpdfstring{Training the model}{Training the model}}\label{md_docs_2project-outline_autotoc_md10}
+\hypertarget{md_docs_2project-outline_autotoc_md11}{}\doxysection{\texorpdfstring{Project structure}{Project structure}}\label{md_docs_2project-outline_autotoc_md11}
 
 \begin{DoxyCode}{0}
 \DoxyCodeLine{ContextSV}
@@ -46,7 +46,7 @@ \chapter{Context\+SV Outline}
 \DoxyCodeLine{\ \ \ \ \ \ \ \ \ \ \ \ └──\ ...}
 
 \end{DoxyCode}
-\hypertarget{md_doc_2project-outline_autotoc_md12}{}\doxysection{\texorpdfstring{Tasks by order}{Tasks by order}}\label{md_doc_2project-outline_autotoc_md12}
+\hypertarget{md_docs_2project-outline_autotoc_md12}{}\doxysection{\texorpdfstring{Tasks by order}{Tasks by order}}\label{md_docs_2project-outline_autotoc_md12}
 
 \begin{DoxyItemize}
 \item \mbox{[}x\mbox{]} Draft project structure
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new file mode 100644
index 00000000..d5da91f8
--- /dev/null
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+\doxysection{docs/project-\/outline.md File Reference}
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 %--- Begin generated contents ---
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