Hdf5 1 12 doxygen merge (#615)

* OESS-98 fix tools test for plugins

* sync fork

* Merge of changes from dev

* Move problem option to bottom of the list until fixed

* HDFFV-11106 - fix parsing optional args

* HDFFV-11106 add note

* grammer fix

* Whitespace after clang formatting

* Undo format version 11 changes

* Update check to working version

* Merge workflow and minor changes from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge serval small changes from dev

* fix typo

* Minor non-space formatting changes

* GH #386 copyright corrections for java folder

* revert because logic requires false return

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Remove case statement for H5I_EVENTSET

* Correct call with versioning

* Remove tabs

* Double underscore change

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
Remove more underscores from header guards

* Merge #380 from develop

* Correct date entry

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* Some Javadoc warning fixes

* Committing clang-format changes

* Updated javadoc fixes

* HDFFV-11228/9 merges from develop

* remove obsolete debug comment

* Fix conflict

* HDFFV-11229 merge changes from develop

* HDFFV-11229 merge second compare from develop

* HDFFV-11229 fix reference file

* HDFFV-11229 update autotools test script for two ref files

* HDFFV-11229 merge dev changes for long double display in tools

* Committing clang-format changes

* Update with changes from develop

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

Update pkgconfig scripts for parallel builds.
Fix install COPYING file reference.
Remove unused round defines.
Change CMake default setting of BUILD_CPP to off.

* Whitespace changes

* Rework CMake add_custom to use the BYPRODUCTS argument

* Revert CMake configure checks for round defines

* With VS 2015 minimum strdup is supported

* Doxygen comments merged from develop

* doxygen build updates

* Correct version string for map functions

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

MANIFEST

@@ -207,7 +207,12 @@
 
 ./doxygen/aliases
 ./doxygen/Doxyfile.in
-./doxygen/dox/api-compat-macros.dox
+./doxygen/dox/About.dox
+./doxygen/dox/Cookbook.dox
+./doxygen/dox/DDLBNF110.dox
+./doxygen/dox/DDLBNF112.dox
+./doxygen/dox/FileFormatSpec.dox
+./doxygen/dox/GettingStarted.dox
 ./doxygen/dox/H5AC_cache_config_t.dox
 ./doxygen/dox/H5Acreate.dox
 ./doxygen/dox/H5Aiterate.dox
@@ -224,12 +229,53 @@
 ./doxygen/dox/H5Ovisit_by_name.dox
 ./doxygen/dox/H5Ovisit.dox
 ./doxygen/dox/H5Sencode.dox
-./doxygen/dox/mainpage.dox
+./doxygen/dox/MetadataCachingInHDF5.dox
+./doxygen/dox/OtherSpecs.dox
+./doxygen/dox/Overview.dox
+./doxygen/dox/ReferenceManual.dox
+./doxygen/dox/Specifications.dox
+./doxygen/dox/TechnicalNotes.dox
+./doxygen/dox/api-compat-macros.dox
+./doxygen/dox/maybe_metadata_reads.dox
 ./doxygen/dox/rm-template.dox
+./doxygen/examples/FF-IH_FileGroup.gif
+./doxygen/examples/FF-IH_FileObject.gif
+./doxygen/examples/FileFormatSpecChunkDiagram.jpg
+./doxygen/examples/H5Pset_metadata_read_attempts.c
+./doxygen/examples/H5Pset_object_flush_cb.c
+./doxygen/examples/H5.format.1.0.html
+./doxygen/examples/H5.format.1.1.html
+./doxygen/examples/H5.format.2.0.html
+./doxygen/examples/H5.format.html
+./doxygen/examples/H5A_examples.c
+./doxygen/examples/H5D_examples.c
 ./doxygen/examples/H5Fclose.c
 ./doxygen/examples/H5Fcreate.c
+./doxygen/examples/H5F_examples.c
+./doxygen/examples/H5Pget_metadata_read_attempts.1.c
+./doxygen/examples/H5Pget_metadata_read_attempts.2.c
+./doxygen/examples/H5Pget_metadata_read_attempts.3.c
+./doxygen/examples/H5Pget_object_flush_cb.c
+./doxygen/examples/ImageSpec.html
+./doxygen/examples/PaletteExample1.gif
+./doxygen/examples/Palettes.fm.anc.gif
+./doxygen/examples/TableSpec.html
+./doxygen/examples/ThreadSafeLibrary.html
+./doxygen/examples/VFL.html
 ./doxygen/examples/hello_hdf5.c
+./doxygen/hdf5_footer.html
+./doxygen/hdf5_header.html
+./doxygen/hdf5_navtree_hacks.js
+./doxygen/hdf5doxy.css
+./doxygen/hdf5doxy_layout.xml
+./doxygen/img/FF-IH_FileGroup.gif
+./doxygen/img/FF-IH_FileObject.gif
+./doxygen/img/FileFormatSpecChunkDiagram.jpg
 ./doxygen/img/HDFG-logo.png
+./doxygen/img/PaletteExample1.gif
+./doxygen/img/Palettes.fm.anc.gif
+./doxygen/img/ftv2node.png
+./doxygen/img/ftv2pnode.png
 
 ./examples/Attributes.txt
 ./examples/Makefile.am

Makefile.am

@@ -35,6 +35,9 @@
 
 include $(top_srcdir)/config/commence.am
 
+# include Doxygen rules (requires autoconf-archive >2016-03-20)
+@DX_RULES@
+
 # Define subdirectories to build.
 ## Automake understands that `make distclean' should recurse into
 ## conditional subdirectories even if `make all' does not.
@@ -187,15 +190,10 @@ check-all-install:
 trace:
 	@(cd src && $(MAKE) $(AM_MAKEFLAGS) $@) || exit 1;
 
-# Run doxygen across source files.
-# Currently, only invoke doxygen in the src directory.
-doxygen:
-	@echo Invoking doxygen
-	for d in src; do                                                \
-	  if test $$d != .; then                                        \
-	    (cd $$d && $(MAKE) $(AM_MAKEFLAGS) $@) || exit 1;           \
-	  fi;                                                           \
-	done
+# doxygen support
+if BUILD_DOXYGEN_CONDITIONAL
+doxygen: doxygen-doc
+endif
 
 # Run tests with different Virtual File Drivers.
 # Currently, only invoke check-vfd in the test directory.

configure.ac

@@ -1117,18 +1117,37 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
   AC_SUBST([DOXYGEN_OPTIMIZE_OUTPUT_FOR_C])
   AC_SUBST([DOXYGEN_MACRO_EXPANSION])
   AC_SUBST([DOXYGEN_OUTPUT_DIRECTORY])
-
+  AC_SUBST([DOXYGEN_EXAMPLES_DIRECTORY])
+  AC_SUBST([DOXYGEN_LAYOUT_FILE])
+  AC_SUBST([DOXYGEN_HTML_HEADER])
+  AC_SUBST([DOXYGEN_HTML_FOOTER])
+  AC_SUBST([DOXYGEN_HTML_EXTRA_STYLESHEET])
+  AC_SUBST([DOXYGEN_HTML_EXTRA_FILES])
+  AC_SUBST([DOXYGEN_SERVER_BASED_SEARCH])
+  AC_SUBST([DOXYGEN_EXTERNAL_SEARCH])
+  AC_SUBST([DOXYGEN_SEARCHENGINE_URL])
+
+# SRCDIR Environment variables used inside doxygen macro for the source location:
   DOXYGEN_PACKAGE=${PACKAGE_NAME}
   DOXYGEN_VERSION_STRING=${PACKAGE_VERSION}
   DOXYGEN_INCLUDE_ALIASES='$(SRCDIR)/doxygen/aliases'
   DOXYGEN_PROJECT_LOGO='$(SRCDIR)/doxygen/img/HDFG-logo.png'
-  DOXYGEN_PROJECT_BRIEF="C-API Reference"
+  DOXYGEN_PROJECT_BRIEF=
   DOXYGEN_INPUT_DIRECTORY='$(SRCDIR) $(SRCDIR)/doxygen/dox'
   DOXYGEN_OPTIMIZE_OUTPUT_FOR_C=YES
   DOXYGEN_MACRO_EXPANSION=YES
   DOXYGEN_OUTPUT_DIRECTORY=hdf5lib_docs
-
-  DX_INIT_DOXYGEN([HDF5], [../doxygen/Doxyfile], [hdf5lib_docs])
+  DOXYGEN_EXAMPLES_DIRECTORY='$(SRCDIR)/doxygen/examples $(SRCDIR)/src $(SRCDIR)/examples $(SRCDIR)/test'
+  DOXYGEN_LAYOUT_FILE='$(SRCDIR)/doxygen/hdf5doxy_layout.xml'
+  DOXYGEN_HTML_HEADER='$(SRCDIR)/doxygen/hdf5_header.html'
+  DOXYGEN_HTML_FOOTER='$(SRCDIR)/doxygen/hdf5_footer.html'
+  DOXYGEN_HTML_EXTRA_STYLESHEET='$(SRCDIR)/doxygen/hdf5doxy.css'
+  DOXYGEN_HTML_EXTRA_FILES='$(SRCDIR)/doxygen/hdf5_navtree_hacks.js $(SRCDIR)/doxygen/img/ftv2node.png $(SRCDIR)/doxygen/img/ftv2pnode.png'
+  DOXYGEN_SERVER_BASED_SEARCH=NO
+  DOXYGEN_EXTERNAL_SEARCH=NO
+  DOXYGEN_SEARCHENGINE_URL=
+
+  DX_INIT_DOXYGEN([HDF5], [./doxygen/Doxyfile], [hdf5lib_docs])
 
 else
   AC_MSG_RESULT([no])

doxygen/Doxyfile.in

@@ -738,7 +738,7 @@ FILE_VERSION_FILTER    =
 # DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
 # tag is left empty.
 
-LAYOUT_FILE            =
+LAYOUT_FILE            = @DOXYGEN_LAYOUT_FILE@
 
 # The CITE_BIB_FILES tag can be used to specify one or more bib files containing
 # the reference definitions. This must be a list of .bib files. The .bib
@@ -855,7 +855,16 @@ INPUT_ENCODING         = UTF-8
 
 FILE_PATTERNS          = H5*public.h \
                          H5*module.h \
+                         H5FDcore.h \
+                         H5FDdirect.h \
+                         H5FDfamily.h \
+                         H5FDlog.h \
+                         H5FDmpi.h \
                          H5FDmpio.h \
+                         H5FDmulti.h \
+                         H5FDsec2.h \
+                         H5FDstdio.h \
+                         H5FDwindows.h \
                          H5VLconnector.h \
                          H5VLconnector_passthru.h \
                          H5VLnative.h \
@@ -908,7 +917,7 @@ EXCLUDE_SYMBOLS        =
 # that contain example code fragments that are included (see the \include
 # command).
 
-EXAMPLE_PATH           = ../src ../examples ../test examples
+EXAMPLE_PATH           = @DOXYGEN_EXAMPLES_DIRECTORY@
 
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
@@ -1169,7 +1178,7 @@ HTML_FILE_EXTENSION    = .html
 # of the possible markers and block names see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_HEADER            =
+HTML_HEADER            = @DOXYGEN_HTML_HEADER@
 
 # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
 # generated HTML page. If the tag is left blank doxygen will generate a standard
@@ -1179,7 +1188,7 @@ HTML_HEADER            =
 # that doxygen normally uses.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_FOOTER            =
+HTML_FOOTER            = @DOXYGEN_HTML_FOOTER@
 
 # The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
 # sheet that is used by each HTML page. It can be used to fine-tune the look of
@@ -1204,7 +1213,7 @@ HTML_STYLESHEET        =
 # list). For an example see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_STYLESHEET  =
+HTML_EXTRA_STYLESHEET  = @DOXYGEN_HTML_EXTRA_STYLESHEET@
 
 # The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
 # other source files which should be copied to the HTML output directory. Note
@@ -1214,7 +1223,7 @@ HTML_EXTRA_STYLESHEET  =
 # files will be copied as-is; there are no commands or markers available.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_FILES       =
+HTML_EXTRA_FILES       = @DOXYGEN_HTML_EXTRA_FILES@
 
 # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
 # will adjust the colors in the style sheet and background images according to
@@ -1272,7 +1281,7 @@ HTML_DYNAMIC_MENUS     = NO
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_DYNAMIC_SECTIONS  = NO
+HTML_DYNAMIC_SECTIONS  = YES
 
 # With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
 # shown in the various tree structured indices initially; the user can expand
@@ -1484,7 +1493,7 @@ ECLIPSE_DOC_ID         = org.doxygen.Project
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-DISABLE_INDEX          = NO
+DISABLE_INDEX          = YES
 
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information. If the tag
@@ -1632,7 +1641,7 @@ MATHJAX_CODEFILE       =
 # The default value is: YES.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-SEARCHENGINE           = NO
+SEARCHENGINE           = YES
 
 # When the SERVER_BASED_SEARCH tag is enabled the search engine will be
 # implemented using a web server instead of a web client using JavaScript. There
@@ -1644,7 +1653,7 @@ SEARCHENGINE           = NO
 # The default value is: NO.
 # This tag requires that the tag SEARCHENGINE is set to YES.
 
-SERVER_BASED_SEARCH    = YES
+SERVER_BASED_SEARCH    = @DOXYGEN_SERVER_BASED_SEARCH@
 
 # When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
 # script for searching. Instead the search results are written to an XML file
@@ -1660,7 +1669,7 @@ SERVER_BASED_SEARCH    = YES
 # The default value is: NO.
 # This tag requires that the tag SEARCHENGINE is set to YES.
 
-EXTERNAL_SEARCH        = NO
+EXTERNAL_SEARCH        = @DOXYGEN_EXTERNAL_SEARCH@
 
 # 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.
@@ -1671,7 +1680,7 @@ EXTERNAL_SEARCH        = NO
 # Searching" for details.
 # This tag requires that the tag SEARCHENGINE is set to YES.
 
-SEARCHENGINE_URL       =
+SEARCHENGINE_URL       = @DOXYGEN_SEARCHENGINE_URL@
 
 # When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
 # search data is written to a file for indexing by an external tool. With the
@@ -2168,7 +2177,7 @@ INCLUDE_FILE_PATTERNS  =
 # recursively expanded use the := operator instead of the = operator.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-PREDEFINED             =
+PREDEFINED             = H5_HAVE_PARALLEL
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
 # tag can be used to specify a list of macro names that should be expanded. The