Hdf5 1 10 doxygen merges (#684)

* HDFFV-10865 - merge from dev, HDFArray perf fix.

* Remove duplicate setting

* Whitespace changes after clang format

* Undo version 11 clang format changes

* Merge CMake changes from develop

* test testing script merge from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge small changes from develop

* Minor non-space formatting changes

* #386 copyright corrections for java folder

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Merge updates

#358 patches from vtk
#361 fix header guard spelling

* format fix

* Fix missing underscore and make H5public.h closer to dev

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup

* format alignment

* Add missing test ref file

* Merge #380 from develop

* Finish java merges from develop

* Fix java issues with tests and javadoc

* Correct use of attribute access plist

* Remove debug code

* Remove unused variable

* Change file access to read only for java tests

* Split clang format operations.

* More javadoc comments

* Remove pre-split setting

* format source

* Change windows TS to use older VS.

* Mostly all javadoc fixes, one argument rename.

* synch file

* Merge of long double fix and compiler flags

* HDFFV-11229 merge changes from develop

* HDFFV-11229 correct test script

* 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

* minor whitespace

* remove unneeded macro

* Committing clang-format changes

* 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.

* Fortran target depends

* Remove incorrect source attribute

* Revert define removal

* printf specifiers and VS2015 min changes

* Committing clang-format changes

* Add time struct

* TRILAB-227 and tools debug merges from develop

* Merge various changes from dev

* Issue #669 remove version from pkgcfg filename

* remove version from h5cc script

* doxygen changes merged from develop

* Committing clang-format changes

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

1 files changed, 23 insertions, 16 deletions

diff --git a/doxygen/Doxyfile.in b/doxygen/Doxyfile.in
index b1b783c..0e41a7b 100644
--- a/doxygen/Doxyfile.in
+++ b/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
@@ -855,9 +855,16 @@ INPUT_ENCODING         = UTF-8
 
 FILE_PATTERNS          = H5*public.h \
                          H5*module.h \
-                         H5VLconnector.h \
-                         H5VLconnector_passthru.h \
-                         H5VLnative.h \
+                         H5FDcore.h \
+                         H5FDdirect.h \
+                         H5FDfamily.h \
+                         H5FDlog.h \
+                         H5FDmpi.h \
+                         H5FDmpio.h \
+                         H5FDmulti.h \
+                         H5FDsec2.h \
+                         H5FDstdio.h \
+                         H5FDwindows.h \
                          H5version.h \
                          *.dox
 
@@ -907,7 +914,7 @@ 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
@@ -1168,7 +1175,7 @@ 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
@@ -1178,7 +1185,7 @@ 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
@@ -1203,7 +1210,7 @@ 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
@@ -1213,7 +1220,7 @@ 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
@@ -1271,7 +1278,7 @@ 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
@@ -1483,7 +1490,7 @@ 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
@@ -1631,7 +1638,7 @@ 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
@@ -1643,7 +1650,7 @@ 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
@@ -1659,7 +1666,7 @@ 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.
@@ -1670,7 +1677,7 @@ 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
@@ -2167,7 +2174,7 @@ 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