doygen adjustments

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

@@ -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])

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

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:

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

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
@@ -789,15 +820,6 @@ H5_DLL herr_t H5Aiterate_by_name(hid_t loc_id, const char *obj_name, H5_index_t
                                  H5_iter_order_t order, hsize_t *idx, H5A_operator2_t op, void *op_data,
                                  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
  *
@@ -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) */

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);
 /**