Merge doxygen2 into develop

MANIFEST

@@ -209,7 +209,12 @@
 
 ./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
@@ -226,12 +231,51 @@
 ./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/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

configure.ac

@@ -95,12 +95,12 @@ AC_CONFIG_COMMANDS([pubconf], [
   sed 's/#define /#define H5_/' <src/H5config.h |\
     sed 's/#undef /#undef H5_/' >pubconf
   if test ! -f src/H5pubconf.h; then
-    /bin/mv -f pubconf src/H5pubconf.h
+    mv -f pubconf src/H5pubconf.h
   elif (diff pubconf src/H5pubconf.h >/dev/null); then
     rm -f pubconf
     echo "src/H5pubconf.h is unchanged"
   else
-    /bin/mv -f pubconf src/H5pubconf.h
+    mv -f pubconf src/H5pubconf.h
   fi
   echo "Post process src/libhdf5.settings"
   sed '/^#/d' < src/libhdf5.settings > libhdf5.settings.TMP
@@ -1116,16 +1116,34 @@ 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])
 
   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) $(SRCDIR)/doxygen/dox'
   DOXYGEN_OPTIMIZE_OUTPUT_FOR_C=YES
   DOXYGEN_MACRO_EXPANSION=YES
   DOXYGEN_OUTPUT_DIRECTORY=hdf5lib_docs
+  DOXYGEN_EXAMPLES_DIRECTORY='$(SRCDIR)/doxygen/examples'
+  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])
 

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           = ../src ../examples ../test @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