doygen adjustments (#614)

* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* OESS-98 fix tools test for plugins

* Keep doxygen comments under 100 chars long - format hint

* Whitespace

* HDFFV-11144 - Reclassify CMake messages

* HDFFV-11099/11100 added help text

* Reworked switch statement to compare string instead

* Fix typo

* Update CDash mode

* Correct name of threadsafe

* Correct option name

* Undo accidental commit

* Note LLVM 10 to 11 format default changes

* Update format plugin

* Undo clang-format version 11 changes

* One more correction

* Update supported platforms

* Revert whitespace changes

* Correct whitespace

* Changes from PR#3

* HDFFV-11213 added option to control gcc10 warnings diagnostics

* HDFFV-11212 Use the new references correctly in JNI utility and tests

* format source

* Fix typo

* Add new test file

* HDFFV-11212 - update test and remove unused arg

* Minor non-space formatting changes

* Use H5I_INVALID_ID instead of "-1"

* source formatting

* add missing testfile, update jni function

* Undo commit of debug code

* remove mislocated file

* Fix h5repack test for handling of fapls and id close

* Update h5diff test files usage text

* HDFFV-11212 add new ref tests for JNI export dataset

* src format update

* Remove blank line typo

* src format typo

* long double requires %Lg

* Another long double foramt specifer S.B. %Lg

* issue with t128bit test

* Windows issue with h5dump and type.

* Fix review issues

* refactor function nesting and fix error checks

* format fixes

* Remove untested functions and javadoc quiet comments

* Restore TRY block.

* Change string append errors to memory exception

* revert to H5_JNI_FATAL_ERROR - support functions need work

* Add assertion error for h5util functions

* remove duplicate function

* format fix

* Revert HD function error handling

* Update copyright comments

* GH #386 java folder copyright corrections

* Whitespace

* GH #359 implement and fix tools 1.6 API usage

* remove excessive comments

* Flip inits to correct ifdef section

* rework ifdef to be simpler

* format issue

* Reformat ifdef inits

* remove static attribute

* format compliance

* Update names

* Revert because logic relies on float not being int

* Changes noticed from creating merge of #412

* Double underscore change

* Correct compiler version variable used

* Remove header guard underscores

* Whitespace cleanup

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* correct window os name

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* HDFFV-11113 long double in tools

* HDFFV-11113 add note

* Disable long double tests for now

* HDFFV-11228 remove arbitrary CMake warning groups.

* Make each flag a string

* Some Javadoc warning fixes

* Updated javadoc fixes

* # WARNING: head commit changed in the meantime

HDFFV-11229 Fix long double usage in tools and java

Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.

* Committing clang-format changes

* HDFFV-11229 Add release note

* HDFFV-11229 windows testfile needed

* fix typo

* Remove non supported message text

* HDFFV-11229 - change ldouble test to check both native and general

* HDFFV-11229 add second file compare

* HDFFV-11229 fix reference file

* HDFFV-11229 autotools check two refs

* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output

* Committing clang-format changes

* Update release note

* Update attribute type of ref file

* Change source of ninja for macs

* try port instead of brew

* Recommended is to use brew.

* Undo non long double changes

* remove unneeded file

* Fix perl and doxygen CMake code

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

* Add stamp files to BYPRODUCTS

* Only one copy of file exists

* Fix custom cmmand depends targets

* Fix fortran custom command DEPENDS

* Add LD_LIBRARY_PATH to tests

* Add custom target for DEPENDS

* Add h5detect conditionaly to generated target DEPENDS

* Correct DEPENDS targets

* Parallel builds need the mpi compiler for pkgconfig scripts.

* install only if MPI build

* Fortran target depends

* Remove incorrect source attribute

* doxygen adjustments

* doxygen build updates

* Correct version

* Correct function version - function has been merged to 1.12

* Correct version string for map functions

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

11 files changed, 112 insertions, 100 deletions

diff --git a/Makefile.am b/Makefile.am
index cc38972..8518114 100644
--- a/Makefile.am
+++ b/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.
diff --git a/configure.ac b/configure.ac
index b6694ad..2df2b90 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1126,6 +1126,7 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
   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='$(SRCDIR)/doxygen/aliases'
@@ -1135,7 +1136,7 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
   DOXYGEN_OPTIMIZE_OUTPUT_FOR_C=YES
   DOXYGEN_MACRO_EXPANSION=YES
   DOXYGEN_OUTPUT_DIRECTORY=hdf5lib_docs
-  DOXYGEN_EXAMPLES_DIRECTORY='$(SRCDIR)/doxygen/examples'
+  DOXYGEN_EXAMPLES_DIRECTORY='$(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'
@@ -1145,7 +1146,7 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
   DOXYGEN_EXTERNAL_SEARCH=NO
   DOXYGEN_SEARCHENGINE_URL=
 
-  DX_INIT_DOXYGEN([HDF5], [../doxygen/Doxyfile], [hdf5lib_docs])
+  DX_INIT_DOXYGEN([HDF5], [./doxygen/Doxyfile], [hdf5lib_docs])
 
 else
   AC_MSG_RESULT([no])
diff --git a/doxygen/Doxyfile.in b/doxygen/Doxyfile.in
index b1cb955..29f3028 100644
--- a/doxygen/Doxyfile.in
+++ b/doxygen/Doxyfile.in
@@ -917,7 +917,7 @@ EXCLUDE_SYMBOLS        =
 # that contain example code fragments that are included (see the \include
 # command).
 
-EXAMPLE_PATH           = ../src ../examples ../test @DOXYGEN_EXAMPLES_DIRECTORY@
+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
diff --git a/release_docs/INSTALL b/release_docs/INSTALL
index 9546615..c9f7d4c 100644
--- a/release_docs/INSTALL
+++ b/release_docs/INSTALL
@@ -450,6 +450,19 @@ CONTENTS
 
             $ make -j -l6
 
+4.4. Building doxygen
+        One can optionally build the doxygen files for the HDF5 C library.
+        By default, this option is disabled. To build the html files, specify
+        '--enable-doxygen'.
+
+            $ ./configure --enable-doxygen
+
+        Configuration will halt if the required applications are not available.
+        To build:
+
+            $ make doxygen
+
+
 4.5. Testing
         HDF5 comes with various test suites, all of which can be run by
         specifying:
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 9bacd6b..b648e26 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1390,8 +1390,8 @@ endif ()
 # Option to build documentation
 #-----------------------------------------------------------------------------
 if (DOXYGEN_FOUND)
-  set (DOXYGEN_PACKAGE ${HDF5_PACKAGE})
-  set (DOXYGEN_VERSION_STRING ${HDF5_VERSION_STRING})
+  set (DOXYGEN_PACKAGE ${HDF5_PACKAGE_NAME})
+  set (DOXYGEN_VERSION_STRING ${HDF5_PACKAGE_VERSION_STRING})
   set (DOXYGEN_INCLUDE_ALIASES_PATH ${HDF5_DOXYGEN_DIR})
   set (DOXYGEN_INCLUDE_ALIASES aliases)
   set (DOXYGEN_VERBATIM_VARS DOXYGEN_INCLUDE_ALIASES)
@@ -1401,7 +1401,15 @@ if (DOXYGEN_FOUND)
   set (DOXYGEN_OPTIMIZE_OUTPUT_FOR_C YES)
   set (DOXYGEN_MACRO_EXPANSION YES)
   set (DOXYGEN_OUTPUT_DIRECTORY ${HDF5_BINARY_DIR}/hdf5lib_docs)
-  set (DOXYGEN_EXAMPLES_DIRECTORY ${HDF5_DOXYGEN_DIR}/examples)
+  set (DOXYGEN_EXAMPLES_DIRECTORY "${HDF5_DOXYGEN_DIR}/examples ${HDF5_SRC_DIR} ${HDF5_SOURCE_DIR}/examples ${HDF5_TEST_SRC_DIR}")
+  set (DOXYGEN_LAYOUT_FILE ${HDF5_DOXYGEN_DIR}/hdf5doxy_layout.xml)
+  set (DOXYGEN_HTML_HEADER ${HDF5_DOXYGEN_DIR}/hdf5_header.html)
+  set (DOXYGEN_HTML_FOOTER ${HDF5_DOXYGEN_DIR}/hdf5_footer.html)
+  set (DOXYGEN_HTML_EXTRA_STYLESHEET ${HDF5_DOXYGEN_DIR}/hdf5doxy.css)
+  set (DOXYGEN_HTML_EXTRA_FILES "${HDF5_DOXYGEN_DIR}/hdf5_navtree_hacks.js ${HDF5_DOXYGEN_DIR}/img/ftv2node.png ${HDF5_DOXYGEN_DIR}/img/ftv2pnode.png")
+  set (DOXYGEN_SERVER_BASED_SEARCH NO)
+  set (DOXYGEN_EXTERNAL_SEARCH NO)
+  set (DOXYGEN_SEARCHENGINE_URL)
 
 # This configure and custom target work together
   # Replace variables inside @@ with the current values
diff --git a/src/H5Apublic.h b/src/H5Apublic.h
index 2d58cdf..b3da77f 100644
--- a/src/H5Apublic.h
+++ b/src/H5Apublic.h
@@ -89,6 +89,13 @@ extern "C" {
  * \see H5Acreate(), H5Aopen()
  */
 H5_DLL herr_t H5Aclose(hid_t attr_id);
+/*--------------------------------------------------------------------------*/
+/**
+ * \ingroup ASYNC
+ * \async_variant_of{H5Aclose}
+ */
+H5_DLL herr_t H5Aclose_async(const char *app_file, const char *app_func, unsigned app_line, hid_t attr_id,
+                             hid_t es_id);
 /* --------------------------------------------------------------------------*/
 /**
  * \ingroup H5A
@@ -195,6 +202,15 @@ H5_DLL hid_t H5Acreate_async(const char *app_file, const char *app_func, unsigne
  */
 H5_DLL hid_t H5Acreate_by_name(hid_t loc_id, const char *obj_name, const char *attr_name, hid_t type_id,
                                hid_t space_id, hid_t acpl_id, hid_t aapl_id, hid_t lapl_id);
+/*--------------------------------------------------------------------------*/
+/**
+ * \ingroup ASYNC
+ * \async_variant_of{H5Acreate_by_name}
+ */
+H5_DLL hid_t H5Acreate_by_name_async(const char *app_file, const char *app_func, unsigned app_line,
+                                     hid_t loc_id, const char *obj_name, const char *attr_name, hid_t type_id,
+                                     hid_t space_id, hid_t acpl_id, hid_t aapl_id, hid_t lapl_id,
+                                     hid_t es_id);
 /*-------------------------------------------------------------------------*/
 /**
  * \ingroup H5A
@@ -316,6 +332,13 @@ H5_DLL herr_t H5Adelete_by_name(hid_t loc_id, const char *obj_name, const char *
  *
  */
 H5_DLL htri_t H5Aexists(hid_t obj_id, const char *attr_name);
+/*--------------------------------------------------------------------------*/
+/**
+ * \ingroup ASYNC
+ * \async_variant_of{H5Aexists}
+ */
+H5_DLL herr_t H5Aexists_async(const char *app_file, const char *app_func, unsigned app_line, hid_t obj_id,
+                              const char *attr_name, hbool_t *exists, hid_t es_id);
 /*-------------------------------------------------------------------------*/
 /**
  * \ingroup H5A
@@ -349,6 +372,14 @@ H5_DLL htri_t H5Aexists(hid_t obj_id, const char *attr_name);
  *
  */
 H5_DLL htri_t H5Aexists_by_name(hid_t obj_id, const char *obj_name, const char *attr_name, hid_t lapl_id);
+/*--------------------------------------------------------------------------*/
+/**
+ * \ingroup ASYNC
+ * \async_variant_of{H5Aexists_by_name}
+ */
+H5_DLL herr_t H5Aexists_by_name_async(const char *app_file, const char *app_func, unsigned app_line,
+                                      hid_t loc_id, const char *obj_name, const char *attr_name,
+                                      hbool_t *exists, hid_t lapl_id, hid_t es_id);
 /*-------------------------------------------------------------------------*/
 /**
  * \ingroup H5A
@@ -790,15 +821,6 @@ H5_DLL herr_t H5Aiterate_by_name(hid_t loc_id, const char *obj_name, H5_index_t
                                  hid_t lapl_id);
 /*--------------------------------------------------------------------------*/
 /**
- * \ingroup ASYNC
- * \async_variant_of{H5Acreate_by_name}
- */
-H5_DLL hid_t H5Acreate_by_name_async(const char *app_file, const char *app_func, unsigned app_line,
-                                     hid_t loc_id, const char *obj_name, const char *attr_name, hid_t type_id,
-                                     hid_t space_id, hid_t acpl_id, hid_t aapl_id, hid_t lapl_id,
-                                     hid_t es_id);
-/*--------------------------------------------------------------------------*/
-/**
  * \ingroup H5A
  *
  * \brief Opens an attribute for an object specified by object identifier and
@@ -969,6 +991,13 @@ H5_DLL hid_t H5Aopen_by_name_async(const char *app_file, const char *app_func, u
  *
  */
 H5_DLL herr_t H5Aread(hid_t attr_id, hid_t type_id, void *buf);
+/*--------------------------------------------------------------------------*/
+/**
+ * \ingroup ASYNC
+ * \async_variant_of{H5Aread}
+ */
+H5_DLL herr_t H5Aread_async(const char *app_file, const char *app_func, unsigned app_line, hid_t attr_id,
+                            hid_t dtype_id, void *buf, hid_t es_id);
 /*-------------------------------------------------------------------------*/
 /**
  * \ingroup H5A
@@ -994,10 +1023,18 @@ H5_DLL herr_t H5Arename(hid_t loc_id, const char *old_name, const char *new_name
 /*--------------------------------------------------------------------------*/
 /**
  * \ingroup ASYNC
- * \async_variant_of{H5Aread}
+ * \async_variant_of{H5Arename}
  */
-H5_DLL herr_t H5Aread_async(const char *app_file, const char *app_func, unsigned app_line, hid_t attr_id,
-                            hid_t dtype_id, void *buf, hid_t es_id);
+H5_DLL herr_t H5Arename_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id,
+                              const char *old_name, const char *new_name, hid_t es_id);
+/*--------------------------------------------------------------------------*/
+/**
+ * \ingroup ASYNC
+ * \async_variant_of{H5Arename_by_name}
+ */
+H5_DLL herr_t H5Arename_by_name_async(const char *app_file, const char *app_func, unsigned app_line,
+                                      hid_t loc_id, const char *obj_name, const char *old_attr_name,
+                                      const char *new_attr_name, hid_t lapl_id, hid_t es_id);
 /*--------------------------------------------------------------------------*/
 /**
  * \ingroup H5A
@@ -1037,36 +1074,6 @@ H5_DLL herr_t H5Awrite(hid_t attr_id, hid_t type_id, const void *buf);
  */
 H5_DLL herr_t H5Awrite_async(const char *app_file, const char *app_func, unsigned app_line, hid_t attr_id,
                              hid_t type_id, const void *buf, hid_t es_id);
-/*--------------------------------------------------------------------------*/
-/**
- * \ingroup ASYNC
- * \async_variant_of{H5Arename}
- */
-H5_DLL herr_t H5Arename_async(const char *app_file, const char *app_func, unsigned app_line, hid_t loc_id,
-                              const char *old_name, const char *new_name, hid_t es_id);
-/*--------------------------------------------------------------------------*/
-/**
- * \ingroup ASYNC
- * \async_variant_of{H5Arename_by_name}
- */
-H5_DLL herr_t H5Arename_by_name_async(const char *app_file, const char *app_func, unsigned app_line,
-                                      hid_t loc_id, const char *obj_name, const char *old_attr_name,
-                                      const char *new_attr_name, hid_t lapl_id, hid_t es_id);
-/*--------------------------------------------------------------------------*/
-/**
- * \ingroup ASYNC
- * \async_variant_of{H5Aexists}
- */
-H5_DLL herr_t H5Aexists_async(const char *app_file, const char *app_func, unsigned app_line, hid_t obj_id,
-                              const char *attr_name, hbool_t *exists, hid_t es_id);
-/*--------------------------------------------------------------------------*/
-/**
- * \ingroup ASYNC
- * \async_variant_of{H5Aexists_by_name}
- */
-H5_DLL herr_t H5Aexists_by_name_async(const char *app_file, const char *app_func, unsigned app_line,
-                                      hid_t loc_id, const char *obj_name, const char *attr_name,
-                                      hbool_t *exists, hid_t lapl_id, hid_t es_id);
 /*-------------------------------------------------------------------------*/
 /**
  * \ingroup H5A
@@ -1092,13 +1099,6 @@ H5_DLL herr_t H5Aexists_by_name_async(const char *app_file, const char *app_func
  */
 H5_DLL herr_t H5Arename_by_name(hid_t loc_id, const char *obj_name, const char *old_attr_name,
                                 const char *new_attr_name, hid_t lapl_id);
-/*--------------------------------------------------------------------------*/
-/**
- * \ingroup ASYNC
- * \async_variant_of{H5Aclose}
- */
-H5_DLL herr_t H5Aclose_async(const char *app_file, const char *app_func, unsigned app_line, hid_t attr_id,
-                             hid_t es_id);
 
 /* API Wrappers for async routines */
 /* (Must be defined _after_ the function prototype) */
diff --git a/src/H5Epublic.h b/src/H5Epublic.h
index 20a2107..ace7700 100644
--- a/src/H5Epublic.h
+++ b/src/H5Epublic.h
@@ -38,9 +38,9 @@ typedef struct H5E_error2_t {
     hid_t cls_id;
     /**< Class ID                           */
     hid_t maj_num;
-    /**< Major error ID		                */
+    /**< Major error ID                        */
     hid_t min_num;
-    /**< Minor error number		            */
+    /**< Minor error number                    */
     unsigned line;
     /**< Line in file where error occurs    */
     const char *func_name;
@@ -308,7 +308,7 @@ H5_DLL hid_t H5Eget_current_stack(void);
  *          If \p close_source_stack is \c TRUE, the source error stack
  *          will be closed.
  *
- * \since 1.8.0
+ * \since 1.13.0
  */
 H5_DLL herr_t H5Eappend_stack(hid_t dst_stack_id, hid_t src_stack_id, hbool_t close_source_stack);
 /**
diff --git a/src/H5Mpublic.h b/src/H5Mpublic.h
index e0be828..3f6bf01 100644
--- a/src/H5Mpublic.h
+++ b/src/H5Mpublic.h
@@ -106,7 +106,7 @@ extern "C" {
  *          name specifies the name of the link to the map object relative to
  *          \p loc_id.
  *
- * \since 1.13.0
+ * \since 1.12.0
  *
  */
 H5_DLL hid_t H5Mcreate(hid_t loc_id, const char *name, hid_t key_type_id, hid_t val_type_id, hid_t lcpl_id,
@@ -127,7 +127,7 @@ H5_DLL hid_t H5Mcreate_async(const char *app_file, const char *app_func, unsigne
  *
  * \details
  *
- * \since 1.13.0
+ * \since 1.12.0
  *
  */
 H5_DLL hid_t H5Mcreate_anon(hid_t loc_id, hid_t key_type_id, hid_t val_type_id, hid_t mcpl_id, hid_t mapl_id);
@@ -147,7 +147,7 @@ H5_DLL hid_t H5Mcreate_anon(hid_t loc_id, hid_t key_type_id, hid_t val_type_id,
  *          H5Mclose() when the application is not longer interested in
  *          accessing it.
  *
- * \since 1.13.0
+ * \since 1.12.0
  *
  */
 H5_DLL hid_t H5Mopen(hid_t loc_id, const char *name, hid_t mapl_id);
@@ -173,7 +173,7 @@ H5_DLL hid_t H5Mopen_async(const char *app_file, const char *app_func, unsigned
  *          It is illegal to subsequently use that same map identifier in calls
  *          to other map functions.
  *
- * \since 1.13.0
+ * \since 1.12.0
  *
  */
 H5_DLL herr_t H5Mclose(hid_t map_id);
@@ -197,7 +197,7 @@ H5_DLL herr_t H5Mclose_async(const char *app_file, const char *app_func, unsigne
  *          map object specified by \p map_id and returns identifier for the
  *          datatype.
  *
- * \since 1.13.0
+ * \since 1.12.0
  *
  */
 H5_DLL hid_t H5Mget_key_type(hid_t map_id);
@@ -214,7 +214,7 @@ H5_DLL hid_t H5Mget_key_type(hid_t map_id);
  *          a map object specified by \p map_id and returns identifier for the
  *          datatype .
  *
- * \since 1.13.0
+ * \since 1.12.0
  *
  */
 H5_DLL hid_t H5Mget_val_type(hid_t map_id);
@@ -230,7 +230,7 @@ H5_DLL hid_t H5Mget_val_type(hid_t map_id);
  * \details H5Mget_create_plist() returns an identifier for a copy of the
  *          creation property list for a map object specified by \p map_id.
  *
- * \since 1.13.0
+ * \since 1.12.0
  *
  */
 H5_DLL hid_t H5Mget_create_plist(hid_t map_id);
@@ -246,7 +246,7 @@ H5_DLL hid_t H5Mget_create_plist(hid_t map_id);
  * \details H5Mget_access_plist() returns an identifier for a copy of the access
  *          property list for a map object specified by \p map_id.
  *
- * \since 1.13.0
+ * \since 1.12.0
  *
  */
 H5_DLL hid_t H5Mget_access_plist(hid_t map_id);
@@ -264,7 +264,7 @@ H5_DLL hid_t H5Mget_access_plist(hid_t map_id);
  * \details H5Mget_count() retrieves the number of key-value pairs stored in a
  *          map specified by map_id.
  *
- * \since 1.13.0
+ * \since 1.12.0
  *
  */
 H5_DLL herr_t H5Mget_count(hid_t map_id, hsize_t *count, hid_t dxpl_id);
@@ -294,7 +294,7 @@ H5_DLL herr_t H5Mget_count(hid_t map_id, hsize_t *count, hid_t dxpl_id);
  *          Any further options can be specified through the property list
  *          \p dxpl_id.
  *
- * \since 1.13.0
+ * \since 1.12.0
  *
  */
 H5_DLL herr_t H5Mput(hid_t map_id, hid_t key_mem_type_id, const void *key, hid_t val_mem_type_id,
@@ -335,7 +335,7 @@ H5_DLL herr_t H5Mput_async(const char *app_file, const char *app_func, unsigned
  *          Any further options can be specified through the property list
  *          \p dxpl_id.
  *
- * \since 1.13.0
+ * \since 1.12.0
  *
  */
 H5_DLL herr_t H5Mget(hid_t map_id, hid_t key_mem_type_id, const void *key, hid_t val_mem_type_id, void *value,
@@ -369,7 +369,7 @@ H5_DLL herr_t H5Mget_async(const char *app_file, const char *app_func, unsigned
  *          Any further options can be specified through the property list
  *          \p dxpl_id.
  *
- * \since 1.13.0
+ * \since 1.12.0
  *
  */
 H5_DLL herr_t H5Mexists(hid_t map_id, hid_t key_mem_type_id, const void *key, hbool_t *exists, hid_t dxpl_id);
@@ -407,7 +407,7 @@ H5_DLL herr_t H5Mexists(hid_t map_id, hid_t key_mem_type_id, const void *key, hb
  *
  *          Any further options can be specified through the property list \p dxpl_id.
  *
- * \since 1.13.0
+ * \since 1.12.0
  *
  */
 H5_DLL herr_t H5Miterate(hid_t map_id, hsize_t *idx, hid_t key_mem_type_id, H5M_iterate_t op, void *op_data,
@@ -448,7 +448,7 @@ H5_DLL herr_t H5Miterate(hid_t map_id, hsize_t *idx, hid_t key_mem_type_id, H5M_
  *
  *          Any further options can be specified through the property list \p dxpl_id.
  *
- * \since 1.13.0
+ * \since 1.12.0
  *
  */
 H5_DLL herr_t H5Miterate_by_name(hid_t loc_id, const char *map_name, hsize_t *idx, hid_t key_mem_type_id,
@@ -473,7 +473,7 @@ H5_DLL herr_t H5Miterate_by_name(hid_t loc_id, const char *map_name, hsize_t *id
  *
  *          Any further options can be specified through the property list \p dxpl_id.
  *
- * \since 1.13.0
+ * \since 1.12.0
  *
  */
 H5_DLL herr_t H5Mdelete(hid_t map_id, hid_t key_mem_type_id, const void *key, hid_t dxpl_id);
diff --git a/src/H5Ppublic.h b/src/H5Ppublic.h
index 6235ac8..5adb05e 100644
--- a/src/H5Ppublic.h
+++ b/src/H5Ppublic.h
@@ -5055,22 +5055,22 @@ H5_DLL herr_t H5Pset_metadata_read_attempts(hid_t plist_id, unsigned attempts);
  *
  * <table>
  *   <tr>
- *     <td>#H5FD_MEM_SUPER</td>	<td>Super block data</td>
+ *     <td>#H5FD_MEM_SUPER</td>    <td>Super block data</td>
  *   </tr>
  *   <tr>
- *     <td>#H5FD_MEM_BTREE</td>	<td>B-tree data</td>
+ *     <td>#H5FD_MEM_BTREE</td>    <td>B-tree data</td>
  *   </tr>
  *   <tr>
- *     <td>#H5FD_MEM_DRAW</td>	<td>Dataset raw data</td>
+ *     <td>#H5FD_MEM_DRAW</td>    <td>Dataset raw data</td>
  *   </tr>
  *   <tr>
- *     <td>#H5FD_MEM_GHEAP</td>	<td>Global heap data</td>
+ *     <td>#H5FD_MEM_GHEAP</td>    <td>Global heap data</td>
  *   </tr>
  *   <tr>
- *     <td>#H5FD_MEM_LHEAP</td>	<td>Local Heap data</td>
+ *     <td>#H5FD_MEM_LHEAP</td>    <td>Local Heap data</td>
  *   </tr>
  *   <tr>
- *     <td>#H5FD_MEM_OHDR</td>	<td>Object header data</td>
+ *     <td>#H5FD_MEM_OHDR</td>    <td>Object header data</td>
  *   </tr>
  * </table>
  *
@@ -8389,7 +8389,7 @@ H5_DLL herr_t H5Pset_local_heap_size_hint(hid_t plist_id, size_t size_hint);
  *          buffer is too small it will be reallocated to a larger size, though
  *          this may result in an additional I/O.
  *
- * \since 1.12.?
+ * \since 1.12.0
  *
  */
 H5_DLL herr_t H5Pset_map_iterate_hints(hid_t mapl_id, size_t key_prefetch_size, size_t key_alloc_size);
@@ -8408,7 +8408,7 @@ H5_DLL herr_t H5Pset_map_iterate_hints(hid_t mapl_id, size_t key_prefetch_size,
  * \details H5Pget_map_iterate() returns the map iterate hints, \p key_prefetch_size
  *          and \p key_alloc_size, as set by H5Pset_map_iterate_hints().
  *
- * \since 1.12.?
+ * \since 1.12.0
  *
  */
 H5_DLL herr_t H5Pget_map_iterate_hints(hid_t mapl_id, size_t *key_prefetch_size /*out*/,
diff --git a/src/H5public.h b/src/H5public.h
index 751abbe..ada15a7 100644
--- a/src/H5public.h
+++ b/src/H5public.h
@@ -511,7 +511,7 @@ H5_DLL herr_t H5open(void);
  *          If the HDF5 library is initialized and closed more than once, the
  *          \p func callback must be registered within each open/close cycle.
  *
- * \since 1.12.1
+ * \since 1.13.0
  */
 H5_DLL herr_t H5atclose(H5_atclose_func_t func, void *ctx);
 /**
@@ -735,7 +735,7 @@ H5_DLL herr_t H5check_version(unsigned majnum, unsigned minnum, unsigned relnum)
  *          after it has been closed.  The value of \p is_terminating is
  *          undefined if this routine fails.
  *
- * \since 1.12.1
+ * \since 1.13.0
  */
 H5_DLL herr_t H5is_library_terminating(hbool_t *is_terminating);
 /**
diff --git a/src/Makefile.am b/src/Makefile.am
index 0b4fa5c..6d5a56e 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -19,9 +19,6 @@
 include $(top_srcdir)/config/commence.am
 include $(top_srcdir)/config/lt_vers.am
 
-# include Doxygen rules (requires autoconf-archive >2016-03-20)
-@DX_RULES@
-
 # How to build H5detect for number format detection.
 # Use -g to force no optimization since many compilers (e.g., Intel) takes
 # a long time to compile it with any optimization on.  H5detect is used
@@ -203,11 +200,6 @@ $(top_srcdir)/src/H5version.h: $(top_srcdir)/src/H5vers.txt
 $(top_srcdir)/src/H5overflow.h: $(top_srcdir)/src/H5overflow.txt
 	perl $(top_srcdir)/bin/make_overflow $?
 
-# doxygen support
-if BUILD_DOXYGEN_CONDITIONAL
-doxygen: doxygen-doc
-endif
-
 # Add TRACE macros to library source files.  This is done via the trace script
 # in the hdf5/bin directory.  If the file contains HDF5 API macros, a "clean"
 # version of the source file is saved with a tilde (~) after its name and