From 9186772092a0ed31a2cc30328cbfefb4e4d5db2e Mon Sep 17 00:00:00 2001 From: albert-github Date: Wed, 18 May 2022 16:47:05 +0200 Subject: Documentation: Doxygen warnings When running doxygen on the sources we get (a.o.) the following warnings: ``` .../gudhi-devel/src/Contraction/include/gudhi/Edge_contraction.h:214: warning: unbalanced grouping commands .../gudhi-devel/src/common/doc/examples.h:3: warning: the name 'Examples' supplied as the argument in the \file statement is not an input file error: bib file .../gudhi-devel/biblio/how_to_cite_gudhi.bib not found! .../gudhi-devel/src/common/doc/installation.h:271: warning: included file biblio/how_to_cite_gudhi.bib is not found. Check your EXAMPLE_PATH ``` This is corrected in the different files and in the settings in src/Doxyfile.in Also there are a number of settings that are obsolete like: ``` warning: Tag 'LATEX_SOURCE_CODE' at line 1835 of file '.../gudhi-devel/build_windows_fork/Doxyfile' has become obsolete. ``` This is corrected in the src/Doxyfile.in file --- src/Contraction/include/gudhi/Edge_contraction.h | 2 +- src/Doxyfile.in | 80 +----------------------- src/common/doc/examples.h | 2 +- 3 files changed, 4 insertions(+), 80 deletions(-) diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h index 6c0f4c78..58d627c2 100644 --- a/src/Contraction/include/gudhi/Edge_contraction.h +++ b/src/Contraction/include/gudhi/Edge_contraction.h @@ -26,6 +26,7 @@ namespace contraction { /** \defgroup contr Edge contraction +@{ \author David Salinas @@ -194,7 +195,6 @@ int main (int argc, char *argv[]) std::clog << "Time to simplify and enumerate simplices:\n"; return EXIT_SUCCESS; -} } \endcode diff --git a/src/Doxyfile.in b/src/Doxyfile.in index ae8db1a3..80ae1709 100644 --- a/src/Doxyfile.in +++ b/src/Doxyfile.in @@ -231,12 +231,6 @@ TAB_SIZE = 2 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 @@ -706,7 +700,7 @@ LAYOUT_FILE = CITE_BIB_FILES = @CMAKE_SOURCE_DIR@/biblio/bibliography.bib \ @CMAKE_SOURCE_DIR@/biblio/how_to_cite_cgal.bib \ - @CMAKE_SOURCE_DIR@/biblio/how_to_cite_gudhi.bib + @CMAKE_CURRENT_BINARY_DIR@/biblio/how_to_cite_gudhi.bib #--------------------------------------------------------------------------- # Configuration options related to warning and progress messages @@ -874,7 +868,7 @@ EXCLUDE_SYMBOLS = # that contain example code fragments that are included (see the \include # command). -EXAMPLE_PATH = @CMAKE_SOURCE_DIR@/biblio/ \ +EXAMPLE_PATH = @CMAKE_CURRENT_BINARY_DIR@ \ @CMAKE_SOURCE_DIR@/data/ \ @GUDHI_DOXYGEN_EXAMPLE_PATH@ @@ -1040,25 +1034,6 @@ USE_HTAGS = NO 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 = - #--------------------------------------------------------------------------- # Configuration options related to the alphabetical class index #--------------------------------------------------------------------------- @@ -1070,13 +1045,6 @@ CLANG_OPTIONS = 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 @@ -1775,16 +1743,6 @@ LATEX_BATCHMODE = NO LATEX_HIDE_INDICES = NO -# If the LATEX_SOURCE_CODE tag is set to YES then doxygen will include source -# code with syntax highlighting in the LaTeX output. -# -# Note that which sources are shown also depends on other settings such as -# SOURCE_BROWSER. -# The default value is: NO. -# This tag requires that the tag GENERATE_LATEX is set to YES. - -LATEX_SOURCE_CODE = NO - # The LATEX_BIB_STYLE tag can be used to specify the style to use for the # bibliography, e.g. plainnat, or ieeetr. See # http://en.wikipedia.org/wiki/BibTeX and \cite for more info. @@ -1857,16 +1815,6 @@ RTF_STYLESHEET_FILE = 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 #--------------------------------------------------------------------------- @@ -1956,15 +1904,6 @@ GENERATE_DOCBOOK = NO 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 #--------------------------------------------------------------------------- @@ -2139,12 +2078,6 @@ EXTERNAL_GROUPS = YES EXTERNAL_PAGES = YES -# The PERL_PATH should be the absolute path and name of the perl script -# interpreter (i.e. the result of 'which perl'). -# The default file (with absolute path) is: /usr/bin/perl. - -PERL_PATH = /usr/bin/perl - #--------------------------------------------------------------------------- # Configuration options related to the dot tool #--------------------------------------------------------------------------- @@ -2158,15 +2091,6 @@ PERL_PATH = /usr/bin/perl CLASS_DIAGRAMS = NO -# You can define message sequence charts within doxygen comments using the \msc -# command. Doxygen will then run the mscgen tool (see: -# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the -# documentation. The MSCGEN_PATH tag allows you to specify the directory where -# the mscgen tool resides. If left empty the tool is assumed to be found in the -# default search path. - -MSCGEN_PATH = - # 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. diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h index 879fb96a..556a24f1 100644 --- a/src/common/doc/examples.h +++ b/src/common/doc/examples.h @@ -1,6 +1,6 @@ // List of GUDHI examples and utils - Doxygen needs at least a file tag to analyse comments // Generated from scripts/cpp_examples_for_doxygen.py -/*! @file Examples +/*! @file * \section Witness_complex_example_section Witness_complex * @example strong_witness_persistence.cpp * @example weak_witness_persistence.cpp -- cgit v1.2.3