Fixing Mathjax font issues

ChangeLog.md

@@ -11,6 +11,7 @@
 - *Documentation*
   - Many typos fixed in documentation using Github Copilot. (David Coeurjolly, [#1829](https://github.com/DGtal-team/DGtal/pull/1829))
   - Global spellcheck and pre-commit. (David Coeurjolly, [#1837](https://github.com/DGtal-team/DGtal/pull/1837))
+  - Upgrade of the doxygen configuration to use MathJax 4. Fixes issue #1845 (David Coeurjolly, [#1846](https://github.com/DGtal-team/DGtal/pull/1846))
 
 - *IO*
   - Upgrading the polyscope backend to 2.6.1 (David Coeurjolly, [#1839](https://github.com/DGtal-team/DGtal/pull/1839))

cmake/CheckDGtalDependencies.cmake

@@ -61,3 +61,9 @@ if (TARGET Eigen3::Eigen)
   set(DGtalLibDependencies ${DGtalLibDependencies} Eigen3::Eigen)
   target_link_libraries(DGtal PUBLIC Eigen3::Eigen)
 endif()
+
+
+# -----------------------------------------------------------------------------
+# Fetching mathjax for the documentation
+# -----------------------------------------------------------------------------
+include(mathjax)

cmake/TargetDoxygenDoc.cmake

@@ -78,12 +78,17 @@ if (DOXYGEN_FOUND)
     endif()
   endif()
 
-
   ADD_CUSTOM_TARGET(doc ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG})
   ADD_CUSTOM_TARGET(doc-Board ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG_BOARD})
   ADD_CUSTOM_TARGET(doc-all ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG})
   ADD_DEPENDENCIES(doc-all doc-Board)
 
+  add_custom_command(TARGET doc POST_BUILD
+    COMMAND ${CMAKE_COMMAND} -E make_directory
+        ${CMAKE_BINARY_DIR}/html/MathJax-4.1.1
+    COMMAND ${CMAKE_COMMAND} -E copy_directory
+        ${mathjax_SOURCE_DIR}
+        ${CMAKE_BINARY_DIR}/html/MathJax-4.1.1)
 #  ADD_CUSTOM_TARGET(doc)
 
   # create a windows help .chm file using hhc.exe

cmake/TargetDoxygenDox.cmake

@@ -54,7 +54,12 @@ if (DOXYGEN_FOUND)
 
 
   add_custom_target(dox ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG_DOX})
-
+  add_custom_command(TARGET doc POST_BUILD
+    COMMAND ${CMAKE_COMMAND} -E make_directory
+        ${CMAKE_BINARY_DIR}/html/MathJax-4.1.1
+    COMMAND ${CMAKE_COMMAND} -E copy_directory
+        ${mathjax_SOURCE_DIR}
+        ${CMAKE_BINARY_DIR}/html/MathJax-4.1.1)
 
   # create a windows help .chm file using hhc.exe
   # HTMLHelp DLL must be in path!

cmake/deps/mathjax.cmake

@@ -0,0 +1,13 @@
+if (TARGET mathjax)
+  return()
+endif()
+
+set(CMAKE_CXX_FLAGS_DEBUG_OLD "${CMAKE_CXX_FLAGS_DEBUG}")
+set(CMAKE_CXX_FLAGS_DEBUG "-w")
+
+CPMAddPackage(
+  NAME mathjax
+  GIT_TAG 4.1.1
+  DOWNLOAD_ONLY TRUE
+  GITHUB_REPOSITORY "mathjax/MathJax"
+)

cmake/doxygen.cmake

@@ -17,5 +17,6 @@ if (NOT EXISTS ${PROJECT_SOURCE_DIR}/doc/html)
   file(MAKE_DIRECTORY ${PROJECT_SOURCE_DIR}/doc/html)
 endif()
 
+
 ## Installation target
 install(DIRECTORY ${PROJECT_SOURCE_DIR}/doc/html DESTINATION ${INSTALL_DOC_PATH})

doc/doxy.config.Board.in

@@ -1,4 +1,4 @@
-# Doxyfile 1.13.2
+# Doxyfile 1.16.1
 
 # This file describes the settings to be used by the documentation system
 # Doxygen (www.doxygen.org) for a project.
@@ -351,6 +351,20 @@ EXTENSION_MAPPING      =
 
 MARKDOWN_SUPPORT       = YES
 
+# If the MARKDOWN_STRICT tag is enabled then Doxygen treats text in comments as
+# Markdown formatted also in cases where Doxygen's native markup format
+# conflicts with that of Markdown. This is only relevant in cases where
+# backticks are used. Doxygen's native markup style allows a single quote to end
+# a text fragment started with a backtick and then treat it as a piece of quoted
+# text, whereas in Markdown such text fragment is treated as verbatim and only
+# ends when a second matching backtick is found. Also, Doxygen's native markup
+# format requires double quotes to be escaped when they appear in a backtick
+# section, whereas this is not needed for Markdown.
+# The default value is: YES.
+# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
+
+MARKDOWN_STRICT        = 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.
@@ -382,8 +396,8 @@ AUTOLINK_SUPPORT       = YES
 
 # This tag specifies a list of words that, when matching the start of a word in
 # the documentation, will suppress auto links generation, if it is enabled via
-# AUTOLINK_SUPPORT. This list does not affect affect links explicitly created
-# using \# or the \link or commands.
+# AUTOLINK_SUPPORT. This list does not affect links explicitly created using #
+# or the \link or \ref commands.
 # This tag requires that the tag AUTOLINK_SUPPORT is set to YES.
 
 AUTOLINK_IGNORE_WORDS  =
@@ -500,7 +514,7 @@ LOOKUP_CACHE_SIZE      = 0
 # which effectively 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.
+# Minimum value: 0, maximum value: 512, default value: 1.
 
 NUM_PROC_THREADS       = 1
 
@@ -769,6 +783,27 @@ GENERATE_BUGLIST       = YES
 
 GENERATE_DEPRECATEDLIST= YES
 
+# The GENERATE_REQUIREMENTS tag can be used to enable (YES) or disable (NO) the
+# requirements page. When enabled, this page is automatically created when at
+# least one comment block with a \requirement command appears in the input.
+# The default value is: YES.
+
+GENERATE_REQUIREMENTS  = YES
+
+# The REQ_TRACEABILITY_INFO tag controls if traceability information is shown on
+# the requirements page (only relevant when using \requirement comment blocks).
+# The setting NO will disable the traceablility information altogether. The
+# setting UNSATISFIED_ONLY will show a list of requirements that are missing a
+# satisfies relation (through the command: \satisfies). Similarly the setting
+# UNVERIFIED_ONLY will show a list of requirements that are missing a verifies
+# relation (through the command: \verifies). Setting the tag to YES (the
+# default) will show both lists if applicable.
+# Possible values are: YES, NO, UNSATISFIED_ONLY and UNVERIFIED_ONLY.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_REQUIREMENTS is set to YES.
+
+REQ_TRACEABILITY_INFO  = 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.
@@ -1016,9 +1051,9 @@ INPUT_FILE_ENCODING    =
 #
 # If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cxxm,
 # *.cpp, *.cppm, *.ccm, *.c++, *.c++m, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl,
-# *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp, *.h++, *.ixx, *.l, *.cs, *.d,
-# *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown, *.md, *.mm, *.dox (to
-# be provided as Doxygen C comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08,
+# *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp, *.h++, *.l, *.cs, *.d, *.php,
+# *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown, *.md, *.mm, *.dox (to be
+# provided as Doxygen C comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08,
 # *.f18, *.f, *.for, *.vhd, *.vhdl, *.ucf, *.qsf and *.ice.
 
 FILE_PATTERNS          = *.cpp \
@@ -1696,7 +1731,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # of each HTML page. A value of NO enables the index and the value YES disables
 # it. Since the tabs in the index contain the same information as the navigation
 # tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
-# The default value is: YES.
+# The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
 DISABLE_INDEX          = NO
@@ -1711,20 +1746,29 @@ DISABLE_INDEX          = NO
 # further fine tune the look of the index (see "Fine-tuning the output"). 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.
+# Since the tree basically has more details information than the tab index, you
+# could consider setting DISABLE_INDEX to YES when enabling this option.
 # The default value is: YES.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
 GENERATE_TREEVIEW      = YES
 
-# When both GENERATE_TREEVIEW and DISABLE_INDEX are set to YES, then the
-# FULL_SIDEBAR option determines if the side bar is limited to only the treeview
-# area (value NO) or if it should extend to the full height of the window (value
-# YES). Setting this to YES gives a layout similar to
-# https://docs.readthedocs.io with more room for contents, but less room for the
-# project logo, title, and description. If either GENERATE_TREEVIEW or
-# DISABLE_INDEX is set to NO, this option has no effect.
+# When GENERATE_TREEVIEW is set to YES, the PAGE_OUTLINE_PANEL option determines
+# if an additional navigation panel is shown at the right hand side of the
+# screen, displaying an outline of the contents of the main page, similar to
+# e.g. https://developer.android.com/reference If GENERATE_TREEVIEW is set to
+# NO, this option has no effect.
+# The default value is: YES.
+# This tag requires that the tag GENERATE_HTML is set to YES.
+
+PAGE_OUTLINE_PANEL     = YES
+
+# When GENERATE_TREEVIEW is set to YES, the FULL_SIDEBAR option determines if
+# the side bar is limited to only the treeview area (value NO) or if it should
+# extend to the full height of the window (value YES). Setting this to YES gives
+# a layout similar to e.g. https://docs.readthedocs.io with more room for
+# contents, but less room for the project logo, title, and description. If
+# GENERATE_TREEVIEW is set to NO, this option has no effect.
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
@@ -1802,25 +1846,26 @@ FORMULA_MACROFILE      =
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-USE_MATHJAX            = NO
+USE_MATHJAX            = YES
 
 # With MATHJAX_VERSION it is possible to specify the MathJax version to be used.
 # Note that the different versions of MathJax have different requirements with
 # regards to the different settings, so it is possible that also other MathJax
 # settings have to be changed when switching between the different MathJax
 # versions.
-# Possible values are: MathJax_2 and MathJax_3.
+# Possible values are: MathJax_2, MathJax_3 and MathJax_4.
 # The default value is: MathJax_2.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_VERSION        = MathJax_2
+MATHJAX_VERSION        = MathJax_4
 
 # When MathJax is enabled you can set the default output format to be used for
 # the MathJax output. For more details about the output format see MathJax
 # version 2 (see:
-# http://docs.mathjax.org/en/v2.7-latest/output.html) and MathJax version 3
+# https://docs.mathjax.org/en/v2.7/output.html), MathJax version 3 (see:
+# https://docs.mathjax.org/en/v3.2/output/index.html) and MathJax version 4
 # (see:
-# http://docs.mathjax.org/en/latest/web/components/output.html).
+# https://docs.mathjax.org/en/v4.0/output/index.htm).
 # Possible values are: HTML-CSS (which is slower, but has the best
 # compatibility. This is the name for Mathjax version 2, for MathJax version 3
 # this will be translated into chtml), NativeMML (i.e. MathML. Only supported
@@ -1833,36 +1878,51 @@ MATHJAX_VERSION        = MathJax_2
 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:
+# output directory using the MATHJAX_RELPATH option. For Mathjax version 2 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.s For Mathjax versions 3
+# and 4 the destination directory should contain the tex-<format>.js script
+# (where <format> is either chtml or svg). 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:
 # - in case of MathJax version 2: https://cdn.jsdelivr.net/npm/mathjax@2
 # - in case of MathJax version 3: https://cdn.jsdelivr.net/npm/mathjax@3
+# - in case of MathJax version 4: https://cdn.jsdelivr.net/npm/mathjax@4
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_RELPATH        = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.3/MathJax.js?config=TeX-MML-AM_CHTML
+MATHJAX_RELPATH        = https://cdn.jsdelivr.net/npm/mathjax@4
 
 # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
 # extension names that should be enabled during MathJax rendering. For example
-# for MathJax version 2 (see
-# https://docs.mathjax.org/en/v2.7-latest/tex.html#tex-and-latex-extensions):
+# for MathJax version 2 (see https://docs.mathjax.org/en/v2.7/tex.html):
 # MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
 # For example for MathJax version 3 (see
-# http://docs.mathjax.org/en/latest/input/tex/extensions/index.html):
+# https://docs.mathjax.org/en/v3.2/input/tex/extensions/):
 # MATHJAX_EXTENSIONS = ams
+# For example for MathJax version 4 (see
+# https://docs.mathjax.org/en/v4.0/input/tex/extensions/):
+# MATHJAX_EXTENSIONS = units
+# Note that for Mathjax version 4 quite a few extensions are already
+# automatically loaded. To disable a package in Mathjax version 4 one can use
+# the package name prepended with a minus sign (- like MATHJAX_EXTENSIONS +=
+# -textmacros)
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_EXTENSIONS     =
+#MATHJAX_EXTENSIONS     = TeX/AMSmath \
+#                         TeX/AMSsymbols
 
 # 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/v2.7-latest/output.html) for more details. For an
-# example see the documentation.
+# of code that will be used on startup of the MathJax code. See the Mathjax site
+# for more details:
+# - MathJax version 2 (see:
+# https://docs.mathjax.org/en/v2.7/)
+# - MathJax version 3 (see:
+# https://docs.mathjax.org/en/v3.2/)
+# - MathJax version 4 (see:
+# https://docs.mathjax.org/en/v4.0/) For an example see the documentation.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
 MATHJAX_CODEFILE       =
@@ -2523,7 +2583,7 @@ HAVE_DOT               = @HAVE_DOT@
 # processors available in the system. You can set it explicitly to a value
 # larger than 0 to get control over the balance between CPU load and processing
 # speed.
-# Minimum value: 0, maximum value: 32, default value: 0.
+# Minimum value: 0, maximum value: 512, default value: 0.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
 DOT_NUM_THREADS        = 0
@@ -2625,6 +2685,15 @@ UML_LOOK               = NO
 
 UML_LIMIT_NUM_FIELDS   = 10
 
+# If the UML_LOOK tag is enabled, field labels are shown along the edge between
+# two class nodes. If there are many fields and many nodes the graph may become
+# too cluttered. The UML_MAX_EDGE_LABELS threshold limits the number of items to
+# make the size more manageable. Set this to 0 for no limit.
+# Minimum value: 0, maximum value: 100, default value: 10.
+# This tag requires that the tag UML_LOOK is set to YES.
+
+UML_MAX_EDGE_LABELS    = 10
+
 # If the DOT_UML_DETAILS tag is set to NO, Doxygen will show attributes and
 # methods without types and arguments in the UML graphs. If the DOT_UML_DETAILS
 # tag is set to YES, Doxygen will add type and arguments for attributes and