Upgrade Doxyfile and add more ignores

.gitignore

@@ -5,3 +5,5 @@ tests/testing_latest/
 tests/testing_bak/
 
 include/sql/*.h
+
+core.sqlite

Doxyfile

@@ -1,4 +1,4 @@
-# Doxyfile 1.8.17
+# Doxyfile 1.8.20
 
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project.
@@ -227,6 +227,14 @@ QT_AUTOBRIEF           = NO
 
 MULTILINE_CPP_IS_BRIEF = NO
 
+# By default Python docstrings are displayed as preformatted text and doxygen's
+# special commands cannot be used. By setting PYTHON_DOCSTRING to NO the
+# doxygen's special commands can be used and the contents of the docstring
+# documentation blocks is shown as doxygen documentation.
+# The default value is: YES.
+
+PYTHON_DOCSTRING       = YES
+
 # 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.
@@ -263,12 +271,6 @@ TAB_SIZE               = 4
 
 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
@@ -310,13 +312,13 @@ OPTIMIZE_OUTPUT_SLICE  = NO
 # extension. Doxygen has a built-in mapping, but you can override or extend it
 # using this tag. The format is ext=language, where ext is a file extension, and
 # language is one of the parsers supported by doxygen: IDL, Java, JavaScript,
-# Csharp (C#), C, C++, D, PHP, md (Markdown), Objective-C, Python, Slice,
+# Csharp (C#), C, C++, D, PHP, md (Markdown), Objective-C, Python, Slice, VHDL,
 # 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
+# default for Fortran type files). For instance to make doxygen treat .inc files
-# .inc files as Fortran files (default is PHP), and .f files as C (default is
+# as Fortran files (default is PHP), and .f files as C (default is Fortran),
-# Fortran), use: inc=Fortran f=C.
+# use: inc=Fortran f=C.
 #
 # Note: For files without extension you can use no_extension as a placeholder.
 #
@@ -455,6 +457,19 @@ TYPEDEF_HIDES_STRUCT   = NO
 
 LOOKUP_CACHE_SIZE      = 0
 
+# The NUM_PROC_THREADS specifies the number threads doxygen is allowed to use
+# during processing. When set to 0 doxygen will based this on the number of
+# cores available in the system. You can set it explicitly to a value larger
+# than 0 to get more control over the balance between CPU load and processing
+# speed. At this moment only the input processing can be done using multiple
+# threads. Since this is still an experimental feature the default is set to 1,
+# which efficively disables parallel processing. Please report any issues you
+# encounter. Generating dot graphs in parallel is controlled by the
+# DOT_NUM_THREADS setting.
+# Minimum value: 0, maximum value: 32, default value: 1.
+
+NUM_PROC_THREADS       = 1
+
 #---------------------------------------------------------------------------
 # Build related configuration options
 #---------------------------------------------------------------------------
@@ -559,7 +574,7 @@ INTERNAL_DOCS          = NO
 # 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.
+# (including Cygwin) and Mac users are advised to set this option to NO.
 # The default value is: system dependent.
 
 CASE_SENSE_NAMES       = NO
@@ -829,7 +844,8 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = .
+INPUT                  = src/ \
+                         include/
 
 # 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
@@ -853,7 +869,7 @@ INPUT_ENCODING         = UTF-8
 # *.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,
+# C comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f18, *.f, *.for, *.vhd,
 # *.vhdl, *.ucf, *.qsf and *.ice.
 
 FILE_PATTERNS          = *.c \
@@ -1378,7 +1394,7 @@ CHM_FILE               =
 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).
+# (YES) or that it should be included in the main .chm file (NO).
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTMLHELP is set to YES.
 
@@ -1514,7 +1530,7 @@ DISABLE_INDEX          = NO
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-GENERATE_TREEVIEW      = NO
+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.
@@ -1540,6 +1556,17 @@ TREEVIEW_WIDTH         = 250
 
 EXT_LINKS_IN_WINDOW    = NO
 
+# If the HTML_FORMULA_FORMAT option is set to svg, doxygen will use the pdf2svg
+# tool (see https://github.com/dawbarton/pdf2svg) or inkscape (see
+# https://inkscape.org) to generate formulas as SVG images instead of PNGs for
+# the HTML output. These images will generally look nicer at scaled resolutions.
+# Possible values are: png (the default) and svg (looks nicer but requires the
+# pdf2svg or inkscape tool).
+# The default value is: png.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+HTML_FORMULA_FORMAT    = png
+
 # 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
@@ -1595,7 +1622,7 @@ MATHJAX_FORMAT         = HTML-CSS
 # 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/.
+# The default value is: https://cdn.jsdelivr.net/npm/mathjax@2.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
 MATHJAX_RELPATH        = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/
@@ -1834,9 +1861,11 @@ LATEX_EXTRA_FILES      =
 
 PDF_HYPERLINKS         = YES
 
-# If the USE_PDFLATEX tag is set to YES, doxygen will use pdflatex to generate
+# If the USE_PDFLATEX tag is set to YES, doxygen will use the engine as
-# the PDF file directly from the LaTeX files. Set this option to YES, to get a
+# specified with LATEX_CMD_NAME to generate the PDF file directly from the LaTeX
-# higher quality PDF documentation.
+# files. Set this option to YES, to get a higher quality PDF documentation.
+#
+# See also section LATEX_CMD_NAME for selecting the engine.
 # The default value is: YES.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
@@ -2075,6 +2104,10 @@ DOCBOOK_PROGRAMLISTING = NO
 
 GENERATE_AUTOGEN_DEF   = NO
 
+#---------------------------------------------------------------------------
+# Configuration options related to Sqlite3 output
+#---------------------------------------------------------------------------
+
 #---------------------------------------------------------------------------
 # Configuration options related to the Perl module output
 #---------------------------------------------------------------------------
@@ -2248,7 +2281,7 @@ EXTERNAL_PAGES         = YES
 # powerful graphs.
 # The default value is: YES.
 
-CLASS_DIAGRAMS         = YES
+CLASS_DIAGRAMS         = NO
 
 # 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
@@ -2270,7 +2303,7 @@ HIDE_UNDOC_RELATIONS   = YES
 # set to NO
 # The default value is: NO.
 
-HAVE_DOT               = NO
+HAVE_DOT               = YES
 
 # The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
 # to run in parallel. When set to 0 doxygen will base this on the number of
@@ -2387,7 +2420,7 @@ INCLUDED_BY_GRAPH      = YES
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-CALL_GRAPH             = NO
+CALL_GRAPH             = YES
 
 # If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
 # dependency graph for every global function or class method.
@@ -2399,7 +2432,7 @@ CALL_GRAPH             = NO
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-CALLER_GRAPH           = NO
+CALLER_GRAPH           = YES
 
 # If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical
 # hierarchy of all classes instead of a textual one.