From a76a6795e71ad41de60fbf6c77d80b8da2c75f30 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Tue, 7 Jun 2022 14:57:23 +0300 Subject: [PATCH 01/10] checking doxygen version --- .github/workflows/run_tests_ubuntu.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests_ubuntu.yml b/.github/workflows/run_tests_ubuntu.yml index a21ac5b001..a04745f870 100644 --- a/.github/workflows/run_tests_ubuntu.yml +++ b/.github/workflows/run_tests_ubuntu.yml @@ -22,7 +22,7 @@ jobs: - name: Install System dependencies shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev + run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen && doxygen --version ### # Installing libhdf4 and libhdf5 From 581b1c1c4d8b28b6ea1316a9aaac599fbed78b7a Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Tue, 7 Jun 2022 15:10:20 +0300 Subject: [PATCH 02/10] updated Doxyfile.in --- .github/workflows/run_tests_ubuntu.yml | 2 +- docs/Doxyfile.in | 813 ++++++++++++++++--------- 2 files changed, 517 insertions(+), 298 deletions(-) diff --git a/.github/workflows/run_tests_ubuntu.yml b/.github/workflows/run_tests_ubuntu.yml index a04745f870..a21ac5b001 100644 --- a/.github/workflows/run_tests_ubuntu.yml +++ b/.github/workflows/run_tests_ubuntu.yml @@ -22,7 +22,7 @@ jobs: - name: Install System dependencies shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen && doxygen --version + run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev ### # Installing libhdf4 and libhdf5 diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in index fec0d0ab7b..6de0c602bb 100644 --- a/docs/Doxyfile.in +++ b/docs/Doxyfile.in @@ -1,3 +1,5 @@ +# Doxyfile 1.8.17 + # This file describes the settings to be used by the documentation system # doxygen (www.doxygen.org) for a project. # @@ -15,11 +17,11 @@ # Project related configuration options #--------------------------------------------------------------------------- -# This tag specifies the encoding used for all characters in the config 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 http://www.gnu.org/software/libiconv -# for the list of possible encodings. +# 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 @@ -44,10 +46,10 @@ PROJECT_NUMBER = @PACKAGE_VERSION@ PROJECT_BRIEF = -# With the PROJECT_LOGO tag one can specify an logo or 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. +# 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 = @abs_top_srcdir@/docs/netcdf-50x50.png @@ -58,7 +60,7 @@ PROJECT_LOGO = @abs_top_srcdir@/docs/netcdf-50x50.png OUTPUT_DIRECTORY = -# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 4096 sub- +# 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 @@ -68,6 +70,14 @@ OUTPUT_DIRECTORY = 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. @@ -83,14 +93,22 @@ CREATE_SUBDIRS = NO OUTPUT_LANGUAGE = English -# If the BRIEF_MEMBER_DESC tag is set to YES doxygen will include brief member +# 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 +# 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 @@ -125,7 +143,7 @@ ALWAYS_DETAILED_SEC = YES INLINE_INHERITED_MEMB = YES -# If the FULL_PATH_NAMES tag is set to YES doxygen will prepend the full path +# 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. @@ -169,6 +187,16 @@ SHORT_NAMES = NO JAVADOC_AUTOBRIEF = YES +# 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 @@ -195,9 +223,9 @@ MULTILINE_CPP_IS_BRIEF = 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. +# 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 @@ -216,10 +244,21 @@ TAB_SIZE = 4 # 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. +# 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 @@ -248,16 +287,28 @@ OPTIMIZE_FOR_FORTRAN = 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, -# C#, C, C++, D, PHP, Objective-C, Python, Fortran, VHDL. 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. +# 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: 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. @@ -266,7 +317,7 @@ 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 http://daringfireball.net/projects/markdown/ for details. +# 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. @@ -274,10 +325,19 @@ EXTENSION_MAPPING = 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 by putting a % sign in front of the word -# or globally by setting AUTOLINK_SUPPORT to NO. +# 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 @@ -299,7 +359,7 @@ BUILTIN_STL_SUPPORT = NO CPP_CLI_SUPPORT = NO # Set the SIP_SUPPORT tag to YES if your project consists of sip (see: -# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen +# 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. @@ -317,13 +377,20 @@ SIP_SUPPORT = NO 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 +# 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 = YES +# 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 @@ -382,7 +449,7 @@ LOOKUP_CACHE_SIZE = 0 # Build related configuration options #--------------------------------------------------------------------------- -# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in +# 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. @@ -392,35 +459,41 @@ LOOKUP_CACHE_SIZE = 0 EXTRACT_ALL = NO -# If the EXTRACT_PRIVATE tag is set to YES all private members of a class will +# 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 = NO -# If the EXTRACT_PACKAGE tag is set to YES all members with package or internal +# 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 +# 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 = YES -# 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 +# 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 = NO -# This flag is only useful for Objective-C code. When set to YES local methods, +# 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 in the documentation. If set to NO, only methods in the interface are # included. # The default value is: NO. @@ -445,21 +518,21 @@ 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. +# 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 -# (class|struct|union) declarations. If set to NO these declarations will be -# included in the documentation. +# 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 +# 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. @@ -473,21 +546,28 @@ HIDE_IN_BODY_DOCS = NO INTERNAL_DOCS = @BUILD_INTERNAL_DOCS@ # 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 +# 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 -# and Mac users are advised to set this option to NO. +# (including Cygwin) ands Mac users are advised to set this option to NO. # The default value is: system dependent. CASE_SENSE_NAMES = YES # 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 +# 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. @@ -515,14 +595,14 @@ 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. +# 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 +# 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. @@ -567,27 +647,25 @@ SORT_BY_SCOPE_NAME = 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 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 = @SHOW_DOXYGEN_TAG_LIST@ -# 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 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 = @SHOW_DOXYGEN_TAG_LIST@ -# The GENERATE_BUGLIST tag can be used to enable ( YES) or disable ( NO) the bug +# 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 = @SHOW_DOXYGEN_TAG_LIST@ -# The GENERATE_DEPRECATEDLIST tag can be used to enable ( YES) or disable ( NO) +# 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. @@ -612,8 +690,8 @@ ENABLED_SECTIONS = @ENABLED_DOC_SECTIONS@ 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 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 @@ -658,11 +736,10 @@ LAYOUT_FILE = @abs_top_srcdir@/docs/DoxygenLayout.xml # 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 http://en.wikipedia.org/wiki/BibTeX for more info. +# 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. Do not use file names with spaces, bibtex cannot handle them. See -# also \cite for info how to create references. +# search path. See also \cite for info how to create references. CITE_BIB_FILES = @@ -678,7 +755,7 @@ CITE_BIB_FILES = QUIET = YES # 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 +# 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. @@ -686,7 +763,7 @@ QUIET = YES WARNINGS = YES -# If the WARN_IF_UNDOCUMENTED tag is set to YES, then doxygen will generate +# 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. @@ -703,12 +780,19 @@ 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. +# 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 = YES +# 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 @@ -732,87 +816,85 @@ WARN_LOGFILE = # 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. +# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING # Note: If this tag is empty the current directory is searched. -INPUT = \ - @abs_top_srcdir@/docs/mainpage.dox \ - @abs_top_srcdir@/RELEASE_NOTES.md \ - @abs_top_srcdir@/docs/install-fortran.md \ - @abs_top_srcdir@/docs/windows-binaries.md \ - @abs_top_srcdir@/docs/attribute_conventions.md \ - @abs_top_srcdir@/docs/file_format_specifications.md \ - @abs_top_srcdir@/docs/inmemory.md \ - @abs_top_srcdir@/docs/filters.md \ - @abs_top_srcdir@/docs/byterange.dox \ - @abs_top_srcdir@/docs/nczarr.md \ - @abs_top_srcdir@/docs/notes.md \ - @abs_top_srcdir@/docs/building-with-cmake.md \ - @abs_top_srcdir@/docs/FAQ.md \ - @abs_top_srcdir@/docs/known_problems.md \ - @abs_top_srcdir@/docs/COPYRIGHT.md \ - @abs_top_srcdir@/docs/credits.md \ - @abs_top_srcdir@/docs/tutorial.dox \ - @abs_top_srcdir@/docs/internal.md \ - @abs_top_srcdir@/docs/dispatch.md \ - @abs_top_srcdir@/docs/inmeminternal.dox \ - @abs_top_srcdir@/docs/indexing.dox \ - @abs_top_srcdir@/docs/testserver.dox \ - @abs_top_srcdir@/docs/quantize.md \ - @abs_top_srcdir@/include/netcdf.h \ - @abs_top_srcdir@/include/netcdf_mem.h \ - @abs_top_srcdir@/include/netcdf_par.h \ - @abs_top_srcdir@/include/netcdf_filter.h \ - @abs_top_srcdir@/libdispatch/dfile.c \ - @abs_top_srcdir@/libdispatch/ddim.c \ - @abs_top_srcdir@/libdispatch/dvar.c \ - @abs_top_srcdir@/libdispatch/dvarget.c \ - @abs_top_srcdir@/libdispatch/dvarinq.c \ - @abs_top_srcdir@/libdispatch/dattinq.c \ - @abs_top_srcdir@/libdispatch/dattget.c \ - @abs_top_srcdir@/libdispatch/dvarput.c \ - @abs_top_srcdir@/libdispatch/dattput.c \ - @abs_top_srcdir@/libdispatch/datt.c \ - @abs_top_srcdir@/libdispatch/dgroup.c \ - @abs_top_srcdir@/libdispatch/dtype.c \ - @abs_top_srcdir@/libdispatch/dcompound.c \ - @abs_top_srcdir@/libdispatch/denum.c \ - @abs_top_srcdir@/libdispatch/dvlen.c \ - @abs_top_srcdir@/libdispatch/dopaque.c \ - @abs_top_srcdir@/libdispatch/dparallel.c \ - @abs_top_srcdir@/libdispatch/derror.c \ - @abs_top_srcdir@/libdispatch/dv2i.c \ - @abs_top_srcdir@/libdispatch/dcopy.c \ - @abs_top_srcdir@/libdispatch/dfilter.c \ - @abs_top_srcdir@/libsrc4/nc4var.c \ - @abs_top_srcdir@/libhdf5/nc4hdf.c \ - @abs_top_srcdir@/libsrc4/nc4internal.c \ - @abs_top_srcdir@/libsrc4/nc4type.c \ - @abs_top_srcdir@/libsrc4/nc4grp.c \ - @abs_top_srcdir@/libsrc4/ncfunc.c \ - @abs_top_srcdir@/libsrc4/nc4dim.c \ - @abs_top_srcdir@/libsrc4/nc4attr.c \ - @abs_top_srcdir@/libsrc4/nc4cache.c \ - @abs_top_srcdir@/libhdf5/nc4info.c \ - @abs_top_srcdir@/libsrc4/nc4dispatch.c \ - @abs_top_srcdir@/libnczarr/zarr.c \ - @abs_top_srcdir@/examples/C/simple_xy_wr.c \ - @abs_top_srcdir@/examples/C/simple_xy_rd.c \ - @abs_top_srcdir@/examples/C/sfc_pres_temp_wr.c \ - @abs_top_srcdir@/examples/C/sfc_pres_temp_rd.c \ - @abs_top_srcdir@/examples/C/pres_temp_4D_wr.c \ - @abs_top_srcdir@/examples/C/pres_temp_4D_rd.c \ - @abs_top_srcdir@/examples/C/simple_nc4_wr.c \ - @abs_top_srcdir@/examples/C/simple_nc4_rd.c \ - @abs_top_srcdir@/examples/C/simple_xy_nc4_wr.c \ - @abs_top_srcdir@/examples/C/simple_xy_nc4_rd.c \ - @abs_top_srcdir@/examples/C/filter_example.c - +INPUT = @abs_top_srcdir@/docs/mainpage.dox \ + @abs_top_srcdir@/RELEASE_NOTES.md \ + @abs_top_srcdir@/docs/install-fortran.md \ + @abs_top_srcdir@/docs/windows-binaries.md \ + @abs_top_srcdir@/docs/attribute_conventions.md \ + @abs_top_srcdir@/docs/file_format_specifications.md \ + @abs_top_srcdir@/docs/inmemory.md \ + @abs_top_srcdir@/docs/filters.md \ + @abs_top_srcdir@/docs/byterange.dox \ + @abs_top_srcdir@/docs/nczarr.md \ + @abs_top_srcdir@/docs/notes.md \ + @abs_top_srcdir@/docs/building-with-cmake.md \ + @abs_top_srcdir@/docs/FAQ.md \ + @abs_top_srcdir@/docs/known_problems.md \ + @abs_top_srcdir@/docs/COPYRIGHT.md \ + @abs_top_srcdir@/docs/credits.md \ + @abs_top_srcdir@/docs/tutorial.dox \ + @abs_top_srcdir@/docs/internal.md \ + @abs_top_srcdir@/docs/dispatch.md \ + @abs_top_srcdir@/docs/inmeminternal.dox \ + @abs_top_srcdir@/docs/indexing.dox \ + @abs_top_srcdir@/docs/testserver.dox \ + @abs_top_srcdir@/docs/quantize.md \ + @abs_top_srcdir@/include/netcdf.h \ + @abs_top_srcdir@/include/netcdf_mem.h \ + @abs_top_srcdir@/include/netcdf_par.h \ + @abs_top_srcdir@/include/netcdf_filter.h \ + @abs_top_srcdir@/libdispatch/dfile.c \ + @abs_top_srcdir@/libdispatch/ddim.c \ + @abs_top_srcdir@/libdispatch/dvar.c \ + @abs_top_srcdir@/libdispatch/dvarget.c \ + @abs_top_srcdir@/libdispatch/dvarinq.c \ + @abs_top_srcdir@/libdispatch/dattinq.c \ + @abs_top_srcdir@/libdispatch/dattget.c \ + @abs_top_srcdir@/libdispatch/dvarput.c \ + @abs_top_srcdir@/libdispatch/dattput.c \ + @abs_top_srcdir@/libdispatch/datt.c \ + @abs_top_srcdir@/libdispatch/dgroup.c \ + @abs_top_srcdir@/libdispatch/dtype.c \ + @abs_top_srcdir@/libdispatch/dcompound.c \ + @abs_top_srcdir@/libdispatch/denum.c \ + @abs_top_srcdir@/libdispatch/dvlen.c \ + @abs_top_srcdir@/libdispatch/dopaque.c \ + @abs_top_srcdir@/libdispatch/dparallel.c \ + @abs_top_srcdir@/libdispatch/derror.c \ + @abs_top_srcdir@/libdispatch/dv2i.c \ + @abs_top_srcdir@/libdispatch/dcopy.c \ + @abs_top_srcdir@/libdispatch/dfilter.c \ + @abs_top_srcdir@/libsrc4/nc4var.c \ + @abs_top_srcdir@/libhdf5/nc4hdf.c \ + @abs_top_srcdir@/libsrc4/nc4internal.c \ + @abs_top_srcdir@/libsrc4/nc4type.c \ + @abs_top_srcdir@/libsrc4/nc4grp.c \ + @abs_top_srcdir@/libsrc4/ncfunc.c \ + @abs_top_srcdir@/libsrc4/nc4dim.c \ + @abs_top_srcdir@/libsrc4/nc4attr.c \ + @abs_top_srcdir@/libsrc4/nc4cache.c \ + @abs_top_srcdir@/libhdf5/nc4info.c \ + @abs_top_srcdir@/libsrc4/nc4dispatch.c \ + @abs_top_srcdir@/libnczarr/zarr.c \ + @abs_top_srcdir@/examples/C/simple_xy_wr.c \ + @abs_top_srcdir@/examples/C/simple_xy_rd.c \ + @abs_top_srcdir@/examples/C/sfc_pres_temp_wr.c \ + @abs_top_srcdir@/examples/C/sfc_pres_temp_rd.c \ + @abs_top_srcdir@/examples/C/pres_temp_4D_wr.c \ + @abs_top_srcdir@/examples/C/pres_temp_4D_rd.c \ + @abs_top_srcdir@/examples/C/simple_nc4_wr.c \ + @abs_top_srcdir@/examples/C/simple_nc4_rd.c \ + @abs_top_srcdir@/examples/C/simple_xy_nc4_wr.c \ + @abs_top_srcdir@/examples/C/simple_xy_nc4_rd.c \ + @abs_top_srcdir@/examples/C/filter_example.c # 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: http://www.gnu.org/software/libiconv) for the list of +# documentation (see: https://www.gnu.org/software/libiconv/) for the list of # possible encodings. # The default value is: UTF-8. @@ -820,12 +902,19 @@ 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. 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, *.py, *.f90, *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf, -# *.qsf, *.as and *.js. +# *.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 = @@ -895,21 +984,21 @@ EXAMPLE_RECURSIVE = NO # that contain images that are to be included in the documentation (see the # \image command). -IMAGE_PATH = @abs_top_srcdir@/docs/images/chunking2.png \ - @abs_top_srcdir@/docs/images/compatibility3.png \ - @abs_top_srcdir@/docs/images/compression.png \ - @abs_top_srcdir@/docs/images/groups.png \ - @abs_top_srcdir@/docs/images/nc4-model.png \ - @abs_top_srcdir@/docs/images/ncatts.png \ - @abs_top_srcdir@/docs/images/nc-classic-uml.png \ - @abs_top_srcdir@/docs/images/nccoords.png \ - @abs_top_srcdir@/docs/images/ncfile.png \ - @abs_top_srcdir@/docs/images/netcdf_architecture.png \ - @abs_top_srcdir@/docs/images/pnetcdf.png \ - @abs_top_srcdir@/docs/images/deptree.jpg \ - @abs_top_srcdir@/docs/images/InstallTreeWindows.png \ - @abs_top_srcdir@/docs/images/quantize_pi.png \ - @abs_top_srcdir@/docs/images/quantize_performance.png +IMAGE_PATH = @abs_top_srcdir@/docs/images/chunking2.png \ + @abs_top_srcdir@/docs/images/compatibility3.png \ + @abs_top_srcdir@/docs/images/compression.png \ + @abs_top_srcdir@/docs/images/groups.png \ + @abs_top_srcdir@/docs/images/nc4-model.png \ + @abs_top_srcdir@/docs/images/ncatts.png \ + @abs_top_srcdir@/docs/images/nc-classic-uml.png \ + @abs_top_srcdir@/docs/images/nccoords.png \ + @abs_top_srcdir@/docs/images/ncfile.png \ + @abs_top_srcdir@/docs/images/netcdf_architecture.png \ + @abs_top_srcdir@/docs/images/pnetcdf.png \ + @abs_top_srcdir@/docs/images/deptree.jpg \ + @abs_top_srcdir@/docs/images/InstallTreeWindows.png \ + @abs_top_srcdir@/docs/images/quantize_pi.png \ + @abs_top_srcdir@/docs/images/quantize_performance.png # 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 @@ -925,6 +1014,10 @@ IMAGE_PATH = @abs_top_srcdir@/docs/images/chunking2.png \ # 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 = @@ -934,11 +1027,15 @@ INPUT_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 +# 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. @@ -986,7 +1083,7 @@ INLINE_SOURCES = NO STRIP_CODE_COMMENTS = YES # If the REFERENCED_BY_RELATION tag is set to YES then for each documented -# function all documented functions referencing it will be listed. +# entity all documented functions referencing it will be listed. # The default value is: NO. REFERENCED_BY_RELATION = NO @@ -998,7 +1095,7 @@ REFERENCED_BY_RELATION = 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 +# 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. @@ -1018,12 +1115,12 @@ 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 http://www.gnu.org/software/global/global.html). You will need version +# (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 config file +# - 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 # @@ -1045,25 +1142,6 @@ 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 -# compiled with the --with-libclang option. -# 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 #--------------------------------------------------------------------------- @@ -1075,6 +1153,13 @@ VERBATIM_HEADERS = YES ALPHABETICAL_INDEX = NO +# 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 @@ -1087,7 +1172,7 @@ IGNORE_PREFIX = # Configuration options related to the HTML output #--------------------------------------------------------------------------- -# If the GENERATE_HTML tag is set to YES doxygen will generate HTML output +# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output # The default value is: YES. GENERATE_HTML = YES @@ -1149,23 +1234,19 @@ HTML_FOOTER = @abs_top_srcdir@/docs/footer.html HTML_STYLESHEET = -# The HTML_EXTRA_STYLESHEET tag can be used to specify an additional user- -# defined cascading style sheet that is included after the standard style sheets +# 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 file to the output directory. For an example -# see the documentation. +# 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 = @DOXYGEN_CSS_FILE@ -# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, -# files or namespaces will be aligned in HTML using tables. If set to -# NO a bullet list will be used. - -# HTML_ALIGN_MEMBERS = YES - # 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 @@ -1177,9 +1258,9 @@ HTML_EXTRA_STYLESHEET = @DOXYGEN_CSS_FILE@ HTML_EXTRA_FILES = images/uniLogo.png # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen -# will adjust the colors in the stylesheet and background images according to +# 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 -# http://en.wikipedia.org/wiki/Hue for more information. For instance the value +# 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. @@ -1208,12 +1289,24 @@ 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 NO can help when comparing the output of multiple runs. -# The default value is: YES. +# 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. @@ -1237,13 +1330,13 @@ 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: http://developer.apple.com/tools/xcode/), introduced with -# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a +# 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 http://developer.apple.com/tools/creatingdocsetswithdoxygen.html -# for more information. +# 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. @@ -1282,7 +1375,7 @@ 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: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on +# (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 @@ -1305,28 +1398,29 @@ GENERATE_HTMLHELP = NO 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 +# 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 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) +# 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. +# 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. @@ -1357,7 +1451,7 @@ 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: http://qt-project.org/doc/qt-4.8/qthelpproject.html#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. @@ -1365,7 +1459,7 @@ 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: http://qt-project.org/doc/qt-4.8/qthelpproject.html#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. @@ -1374,7 +1468,7 @@ 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: http://qt-project.org/doc/qt-4.8/qthelpproject.html#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. @@ -1382,7 +1476,7 @@ 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: http://qt-project.org/doc/qt-4.8/qthelpproject.html#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. @@ -1390,7 +1484,7 @@ 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: -# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes). +# 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 = @@ -1434,12 +1528,19 @@ ECLIPSE_DOC_ID = org.doxygen.Project 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. +# 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 @@ -1460,7 +1561,7 @@ ENUM_VALUES_PER_LINE = 4 TREEVIEW_WIDTH = 250 -# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open links to +# 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. @@ -1476,7 +1577,7 @@ EXT_LINKS_IN_WINDOW = NO FORMULA_FONTSIZE = 10 -# Use the FORMULA_TRANPARENT tag to determine whether or not the images +# 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. # @@ -1487,9 +1588,15 @@ FORMULA_FONTSIZE = 10 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 -# http://www.mathjax.org) which uses client side Javascript for the rendering -# instead of using prerendered bitmaps. Use this if you do not have LaTeX +# 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. @@ -1515,8 +1622,8 @@ MATHJAX_FORMAT = HTML-CSS # 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 http://www.mathjax.org before deployment. -# The default value is: http://cdn.mathjax.org/mathjax/latest. +# 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 = http://cdn.mathjax.org/mathjax/latest @@ -1558,12 +1665,12 @@ MATHJAX_CODEFILE = SEARCHENGINE = @DOXYGEN_SEARCHENGINE@ # 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 flavours 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. +# 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. @@ -1575,9 +1682,9 @@ SERVER_BASED_SEARCH = @DOXYGEN_SERVER_BASED_SEARCH@ # 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 +# Doxygen ships with an example indexer (doxyindexer) and search engine # (doxysearch.cgi) which are based on the open source search engine library -# Xapian (see: http://xapian.org/). +# Xapian (see: https://xapian.org/). # # See the section "External Indexing and Searching" for details. # The default value is: NO. @@ -1588,9 +1695,9 @@ 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 +# Doxygen ships with an example indexer (doxyindexer) and search engine # (doxysearch.cgi) which are based on the open source search engine library -# Xapian (see: http://xapian.org/). See the section "External Indexing and +# 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. @@ -1626,7 +1733,7 @@ EXTRA_SEARCH_MAPPINGS = # Configuration options related to the LaTeX output #--------------------------------------------------------------------------- -# If the GENERATE_LATEX tag is set to YES doxygen will generate LaTeX output. +# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output. # The default value is: YES. GENERATE_LATEX = @NC_ENABLE_DOXYGEN_PDF_OUTPUT@ @@ -1642,22 +1749,36 @@ LATEX_OUTPUT = latex_main # The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be # invoked. # -# Note that when enabling USE_PDFLATEX this option is only used for generating -# bitmaps for formulas in the HTML output, but not in the Makefile that is -# written to the output directory. -# The default file is: latex. +# 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 = latex # 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 -# If the COMPACT_LATEX tag is set to YES doxygen generates more compact LaTeX +# 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. @@ -1675,9 +1796,12 @@ COMPACT_LATEX = NO 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. To get the times font for -# instance you can specify -# EXTRA_PACKAGES=times +# 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. @@ -1691,23 +1815,36 @@ EXTRA_PACKAGES = # # 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. Doxygen will -# replace them by respectively the title of the page, the current date and time, -# only the current date, the version number of doxygen, the project name (see -# PROJECT_NAME), or the project number (see PROJECT_NUMBER). +# $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. +# 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 @@ -1725,8 +1862,8 @@ LATEX_EXTRA_FILES = PDF_HYPERLINKS = YES -# If the LATEX_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 +# 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. @@ -1749,19 +1886,45 @@ 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. +# 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 +# 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. @@ -1776,7 +1939,7 @@ GENERATE_RTF = NO RTF_OUTPUT = rtf -# If the COMPACT_RTF tag is set to YES doxygen generates more compact 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. @@ -1796,9 +1959,9 @@ COMPACT_RTF = NO RTF_HYPERLINKS = NO -# Load stylesheet definitions from file. Syntax is similar to doxygen's config -# file, i.e. a series of assignments. You only have to provide replacements, -# missing definitions are set to their default value. +# 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. @@ -1807,17 +1970,27 @@ RTF_HYPERLINKS = NO RTF_STYLESHEET_FILE = # Set optional variables used in the generation of an RTF document. Syntax is -# similar to doxygen's config file. A template extensions file can be generated -# using doxygen -e rtf extensionFile. +# 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 +# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for # classes and files. # The default value is: NO. @@ -1841,6 +2014,13 @@ MAN_OUTPUT = man 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 @@ -1854,7 +2034,7 @@ MAN_LINKS = YES # Configuration options related to the XML output #--------------------------------------------------------------------------- -# If the GENERATE_XML tag is set to YES doxygen will generate an XML file that +# 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. @@ -1868,7 +2048,7 @@ GENERATE_XML = NO XML_OUTPUT = xml -# If the XML_PROGRAMLISTING tag is set to YES doxygen will dump the program +# 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. @@ -1877,11 +2057,18 @@ XML_OUTPUT = xml 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 +# 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. @@ -1895,14 +2082,23 @@ 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 #--------------------------------------------------------------------------- -# If the GENERATE_AUTOGEN_DEF tag is set to YES doxygen will generate an AutoGen -# Definitions (see http://autogen.sf.net) file that captures the structure of -# the code including all documentation. Note that this feature is still -# experimental and incomplete at the moment. +# 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 @@ -1911,7 +2107,7 @@ 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 +# 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. @@ -1919,7 +2115,7 @@ GENERATE_AUTOGEN_DEF = NO GENERATE_PERLMOD = NO -# If the PERLMOD_LATEX tag is set to YES doxygen will generate the necessary +# 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. @@ -1927,9 +2123,9 @@ GENERATE_PERLMOD = NO PERLMOD_LATEX = NO -# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be nicely +# 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 +# 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. @@ -1949,14 +2145,14 @@ PERLMOD_MAKEVAR_PREFIX = # Configuration options related to the preprocessor #--------------------------------------------------------------------------- -# If the ENABLE_PREPROCESSING tag is set to YES doxygen will evaluate all +# 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 +# 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. @@ -1972,7 +2168,7 @@ MACRO_EXPANSION = NO EXPAND_ONLY_PREDEF = NO -# If the SEARCH_INCLUDES tag is set to YES the includes files in the +# 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. @@ -2014,9 +2210,9 @@ PREDEFINED = USE_NETCDF4 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 +# 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. @@ -2036,13 +2232,11 @@ SKIP_FUNCTION_MACROS = YES # 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 an unique name (where the name does NOT include +# 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 = html/guide.tag=./html_guide "html/tutorial.tag = ./html_tutorial" -#TAGFILES = ../../NUG/html/nug.tag=../../../NUG/html -#TAGFILES = ../../NUG/html/nug.tag=https://docs.unidata.ucar.edu/nug +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 @@ -2050,20 +2244,21 @@ SKIP_FUNCTION_MACROS = YES GENERATE_TAGFILE = html/netcdf-c.tag -# 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. +# 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 +# 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 = NO -# If the EXTERNAL_PAGES tag is set to YES all external pages will be listed in +# 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. @@ -2074,7 +2269,7 @@ EXTERNAL_PAGES = NO # Configuration options related to the dot tool #--------------------------------------------------------------------------- -# If the CLASS_DIAGRAMS tag is set to YES doxygen will generate a class diagram +# 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 @@ -2090,7 +2285,7 @@ CLASS_DIAGRAMS = YES DIA_PATH = -# If set to YES, the inheritance and collaboration graphs will hide inheritance +# 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. @@ -2115,7 +2310,7 @@ HAVE_DOT = @HAVE_DOT@ DOT_NUM_THREADS = 0 -# When you want a differently looking font n the dot files that doxygen +# When you want a differently looking font in the dot files that doxygen # generates you can specify the font name using DOT_FONTNAME. You need to make # sure dot is able to find the font, which can be done by putting it in a # standard location or by setting the DOTFONTPATH environment variable or by @@ -2163,7 +2358,7 @@ COLLABORATION_GRAPH = YES GROUP_GRAPHS = YES -# If the UML_LOOK tag is set to YES doxygen will generate inheritance and +# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and # collaboration diagrams in a style similar to the OMG's Unified Modeling # Language. # The default value is: NO. @@ -2215,7 +2410,8 @@ INCLUDED_BY_GRAPH = YES # # Note that enabling this option will significantly increase the time of a run. # So in most cases it will be better to enable call graphs for selected -# functions only using the \callgraph command. +# functions only using the \callgraph command. Disabling a call graph can be +# accomplished by means of the command \hidecallgraph. # The default value is: NO. # This tag requires that the tag HAVE_DOT is set to YES. @@ -2226,7 +2422,8 @@ CALL_GRAPH = NO # # Note that enabling this option will significantly increase the time of a run. # So in most cases it will be better to enable caller graphs for selected -# functions only using the \callergraph command. +# functions only using the \callergraph command. Disabling a caller graph can be +# accomplished by means of the command \hidecallergraph. # The default value is: NO. # This tag requires that the tag HAVE_DOT is set to YES. @@ -2249,11 +2446,15 @@ GRAPHICAL_HIERARCHY = YES DIRECTORY_GRAPH = YES # The DOT_IMAGE_FORMAT tag can be used to set the image format of the images -# generated by dot. +# generated by dot. For an explanation of the image formats see the section +# output formats in the documentation of the dot tool (Graphviz (see: +# http://www.graphviz.org/)). # Note: If you choose svg you need to set HTML_FILE_EXTENSION to xhtml in order # to make the SVG files visible in IE 9+ (other browsers do not have this # requirement). -# Possible values are: png, jpg, gif and svg. +# Possible values are: png, jpg, gif, svg, png:gd, png:gd:gd, png:cairo, +# png:cairo:gd, png:cairo:cairo, png:cairo:gdiplus, png:gdiplus and +# png:gdiplus:gdiplus. # The default value is: png. # This tag requires that the tag HAVE_DOT is set to YES. @@ -2296,6 +2497,24 @@ MSCFILE_DIRS = DIAFILE_DIRS = +# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the +# path where java can find the plantuml.jar file. If left blank, it is assumed +# PlantUML is not used or called during a preprocessing step. Doxygen will +# generate a warning when it encounters a \startuml command in this case and +# will not generate output for the diagram. + +PLANTUML_JAR_PATH = + +# When using plantuml, the PLANTUML_CFG_FILE tag can be used to specify a +# configuration file for plantuml. + +PLANTUML_CFG_FILE = + +# When using plantuml, the specified paths are searched for files specified by +# the !include statement in a plantuml block. + +PLANTUML_INCLUDE_PATH = + # The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes # that will be shown in the graph. If the number of nodes in a graph becomes # larger than this value, doxygen will truncate the graph, which is visualized @@ -2332,7 +2551,7 @@ MAX_DOT_GRAPH_DEPTH = 0 DOT_TRANSPARENT = NO -# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output +# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output # files in one run (i.e. multiple -o and -T options on the command line). This # makes dot run faster, but since only newer versions of dot (>1.8.10) support # this, this feature is disabled by default. @@ -2349,7 +2568,7 @@ DOT_MULTI_TARGETS = NO GENERATE_LEGEND = YES -# If the DOT_CLEANUP tag is set to YES doxygen will remove the intermediate dot +# If the DOT_CLEANUP tag is set to YES, doxygen will remove the intermediate dot # files that are used to generate the various graphs. # The default value is: YES. # This tag requires that the tag HAVE_DOT is set to YES. From c051209f8b8ba25a508070cd5080d21074419628 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Tue, 7 Jun 2022 15:24:21 +0300 Subject: [PATCH 03/10] turned on WARN_AS_ERROR and added documentation build to CI --- .github/workflows/run_tests_ubuntu.yml | 6 +++--- docs/Doxyfile.in | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/run_tests_ubuntu.yml b/.github/workflows/run_tests_ubuntu.yml index a21ac5b001..dd7b506367 100644 --- a/.github/workflows/run_tests_ubuntu.yml +++ b/.github/workflows/run_tests_ubuntu.yml @@ -22,7 +22,7 @@ jobs: - name: Install System dependencies shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev + run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen ### # Installing libhdf4 and libhdf5 @@ -42,7 +42,7 @@ jobs: wget https://support.hdfgroup.org/ftp/HDF/releases/HDF4.2.15/src/hdf-4.2.15.tar.bz2 tar -jxf hdf-4.2.15.tar.bz2 pushd hdf-4.2.15 - ./configure --prefix=${HOME}/environments/${{ matrix.hdf5 }} --disable-static --enable-shared --disable-fortran --disable-netcdf --with-szlib + ./configure --prefix=${HOME}/environments/${{ matrix.hdf5 }} --disable-static --enable-shared --disable-fortran --disable-netcdf --with-szlib make -j make install -j popd @@ -164,7 +164,7 @@ jobs: - name: Configure shell: bash -l {0} - run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --enable-hdf4 --enable-hdf5 --enable-dap --disable-dap-remote-tests + run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --enable-hdf4 --enable-hdf5 --enable-dap --disable-dap-remote-tests --enable-doxygen if: ${{ success() }} - name: Look at config.log if error diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in index 6de0c602bb..7d1ed90232 100644 --- a/docs/Doxyfile.in +++ b/docs/Doxyfile.in @@ -791,7 +791,7 @@ WARN_NO_PARAMDOC = YES # a warning is encountered. # The default value is: NO. -WARN_AS_ERROR = NO +WARN_AS_ERROR = YES # The WARN_FORMAT tag determines the format of the warning messages that doxygen # can produce. The string should contain the $file, $line, and $text tags, which From c0ffb1eb9d2caa3fae3af5a56b49321f4807ed6e Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Tue, 7 Jun 2022 15:38:01 +0300 Subject: [PATCH 04/10] fixed case of --enable-doxygen but doxygen not found --- configure.ac | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/configure.ac b/configure.ac index 94aaab9348..ce66a3cbdb 100644 --- a/configure.ac +++ b/configure.ac @@ -1075,7 +1075,7 @@ fi # Is doxygen installed? If so, have configure construct the Doxyfile. AC_CHECK_PROGS([DOXYGEN], [doxygen]) if test -z "$DOXYGEN"; then - AC_MSG_WARN([Doxygen not found - documentation will not be built]) + AC_MSG_ERROR([Doxygen not found - install doxygen or build without --enable-doxygen]) fi # Is graphviz/dot installed? If so, we'll use dot to create From aa7e07007cd9365ce5c4993f959a20c4e99dd28d Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Tue, 7 Jun 2022 15:40:24 +0300 Subject: [PATCH 05/10] installing doxygen in CI when needed --- .github/workflows/run_tests_ubuntu.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/run_tests_ubuntu.yml b/.github/workflows/run_tests_ubuntu.yml index dd7b506367..74b8a69c0f 100644 --- a/.github/workflows/run_tests_ubuntu.yml +++ b/.github/workflows/run_tests_ubuntu.yml @@ -69,7 +69,7 @@ jobs: - name: Install System dependencies shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev mpich libmpich-dev + run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev mpich libmpich-dev doxygen ### # Installing libhdf4 and libhdf5 @@ -128,7 +128,7 @@ jobs: - name: Install System dependencies shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev + run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen ### # Set Environmental Variables @@ -208,7 +208,7 @@ jobs: - name: Install System dependencies shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev mpich libmpich-dev + run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev mpich libmpich-dev doxygen ### # Set Environmental Variables @@ -289,7 +289,7 @@ jobs: - name: Install System dependencies shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev + run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen ### # Set Environmental Variables From 981f452952f796585e23b8b28681b4cbc892dbc5 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Tue, 7 Jun 2022 15:55:18 +0300 Subject: [PATCH 06/10] installing doxygen in CI when needed --- .github/workflows/run_tests_ubuntu.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/run_tests_ubuntu.yml b/.github/workflows/run_tests_ubuntu.yml index 74b8a69c0f..86574ce3e7 100644 --- a/.github/workflows/run_tests_ubuntu.yml +++ b/.github/workflows/run_tests_ubuntu.yml @@ -69,7 +69,7 @@ jobs: - name: Install System dependencies shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev mpich libmpich-dev doxygen + run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev mpich libmpich-dev ### # Installing libhdf4 and libhdf5 @@ -164,7 +164,7 @@ jobs: - name: Configure shell: bash -l {0} - run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --enable-hdf4 --enable-hdf5 --enable-dap --disable-dap-remote-tests --enable-doxygen + run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --enable-hdf4 --enable-hdf5 --enable-dap --disable-dap-remote-tests if: ${{ success() }} - name: Look at config.log if error @@ -208,7 +208,7 @@ jobs: - name: Install System dependencies shell: bash -l {0} - run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev mpich libmpich-dev doxygen + run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev mpich libmpich-dev ### # Set Environmental Variables @@ -240,7 +240,7 @@ jobs: - name: Configure shell: bash -l {0} - run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} CC=mpicc ./configure --enable-hdf4 --enable-hdf5 --enable-dap --disable-dap-remote-tests --enable-parallel-tests --enable-pnetcdf + run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} CC=mpicc ./configure --enable-hdf4 --enable-hdf5 --enable-dap --disable-dap-remote-tests --enable-parallel-tests --enable-pnetcdf --enable-doxygen if: ${{ success() }} - name: Look at config.log if error From e3ccb4a22c8668f02bb3e4dc2736f86cea37c874 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Tue, 7 Jun 2022 16:01:07 +0300 Subject: [PATCH 07/10] installing doxygen in CI when needed --- .github/workflows/run_tests_ubuntu.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/run_tests_ubuntu.yml b/.github/workflows/run_tests_ubuntu.yml index 86574ce3e7..0700b1b83d 100644 --- a/.github/workflows/run_tests_ubuntu.yml +++ b/.github/workflows/run_tests_ubuntu.yml @@ -164,7 +164,7 @@ jobs: - name: Configure shell: bash -l {0} - run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --enable-hdf4 --enable-hdf5 --enable-dap --disable-dap-remote-tests + run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --enable-hdf4 --enable-hdf5 --enable-dap --disable-dap-remote-tests --enable-doxygen if: ${{ success() }} - name: Look at config.log if error @@ -240,7 +240,7 @@ jobs: - name: Configure shell: bash -l {0} - run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} CC=mpicc ./configure --enable-hdf4 --enable-hdf5 --enable-dap --disable-dap-remote-tests --enable-parallel-tests --enable-pnetcdf --enable-doxygen + run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} CC=mpicc ./configure --enable-hdf4 --enable-hdf5 --enable-dap --disable-dap-remote-tests --enable-parallel-tests --enable-pnetcdf if: ${{ success() }} - name: Look at config.log if error From 71c6046ca10ba4aae86aff2adb77f09cd8660310 Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Tue, 7 Jun 2022 16:06:10 +0300 Subject: [PATCH 08/10] installing doxygen in CI when needed --- configure.ac | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/configure.ac b/configure.ac index ce66a3cbdb..2e03115dcc 100644 --- a/configure.ac +++ b/configure.ac @@ -1072,10 +1072,12 @@ if test -z "$NC_M4"; then AC_MSG_ERROR([Cannot find m4 utility. Install m4 and try again.]) fi -# Is doxygen installed? If so, have configure construct the Doxyfile. -AC_CHECK_PROGS([DOXYGEN], [doxygen]) -if test -z "$DOXYGEN"; then - AC_MSG_ERROR([Doxygen not found - install doxygen or build without --enable-doxygen]) +if test "x$enable_doxygen" != xno; then + # Is doxygen installed? If so, have configure construct the Doxyfile. + AC_CHECK_PROGS([DOXYGEN], [doxygen]) + if test -z "$DOXYGEN"; then + AC_MSG_ERROR([Doxygen not found - install doxygen or build without --enable-doxygen]) + fi fi # Is graphviz/dot installed? If so, we'll use dot to create From 1e8b98bd064b27742701d9459dde9953f207cf7f Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Tue, 7 Jun 2022 18:04:15 +0300 Subject: [PATCH 09/10] installing doxygen in CI when needed --- .github/workflows/run_tests_ubuntu.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests_ubuntu.yml b/.github/workflows/run_tests_ubuntu.yml index 0700b1b83d..1be7197213 100644 --- a/.github/workflows/run_tests_ubuntu.yml +++ b/.github/workflows/run_tests_ubuntu.yml @@ -164,7 +164,7 @@ jobs: - name: Configure shell: bash -l {0} - run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --enable-hdf4 --enable-hdf5 --enable-dap --disable-dap-remote-tests --enable-doxygen + run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --enable-hdf4 --enable-hdf5 --enable-dap --disable-dap-remote-tests --enable-doxygen if: ${{ success() }} - name: Look at config.log if error From ce767aec2310ab5bea1bbc09d62bbc531b0d09fd Mon Sep 17 00:00:00 2001 From: Edward Hartnett Date: Wed, 8 Jun 2022 07:08:21 +0300 Subject: [PATCH 10/10] change to trigger CI --- .github/workflows/run_tests_ubuntu.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/run_tests_ubuntu.yml b/.github/workflows/run_tests_ubuntu.yml index 1be7197213..0700b1b83d 100644 --- a/.github/workflows/run_tests_ubuntu.yml +++ b/.github/workflows/run_tests_ubuntu.yml @@ -164,7 +164,7 @@ jobs: - name: Configure shell: bash -l {0} - run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --enable-hdf4 --enable-hdf5 --enable-dap --disable-dap-remote-tests --enable-doxygen + run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --enable-hdf4 --enable-hdf5 --enable-dap --disable-dap-remote-tests --enable-doxygen if: ${{ success() }} - name: Look at config.log if error