Remove most unused options which are defaulted HDFGroup#2998

configure.ac

@@ -1237,9 +1237,11 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
   DOXYGEN_PACKAGE=${PACKAGE_NAME}
   DOXYGEN_VERSION_STRING=${PACKAGE_VERSION}
   DOXYGEN_DIR='$(SRCDIR)/doxygen'
+  DOXYGEN_INCLUDE_ALIASES_PATH='$(SRCDIR)/doxygen'
   DOXYGEN_INCLUDE_ALIASES='$(SRCDIR)/doxygen/aliases'
+  DOXYGEN_VERBATIM_VARS='DOXYGEN_INCLUDE_ALIASES'
   DOXYGEN_PROJECT_LOGO='$(SRCDIR)/doxygen/img/HDFG-logo.png'
-  DOXYGEN_PROJECT_BRIEF=''
+  DOXYGEN_PROJECT_BRIEF='API Reference'
   DOXYGEN_INPUT_DIRECTORY='$(SRCDIR) $(SRCDIR)/doxygen/dox'
   DOXYGEN_OPTIMIZE_OUTPUT_FOR_C=YES
   DOXYGEN_MACRO_EXPANSION=YES
@@ -1256,7 +1258,7 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
   DOXYGEN_SEARCHENGINE_URL=
   DOXYGEN_STRIP_FROM_PATH='$(SRCDIR)'
   DOXYGEN_STRIP_FROM_INC_PATH='$(SRCDIR)'
-  DOXYGEN_PREDEFINED='H5_HAVE_DIRECT H5_HAVE_LIBHDFS H5_HAVE_MAP_API H5_HAVE_PARALLEL H5_HAVE_ROS3_VFD H5_DOXYGEN_FORTRAN'
+  DOXYGEN_PREDEFINED='H5_HAVE_DIRECT H5_HAVE_LIBHDFS H5_HAVE_MAP_API H5_HAVE_PARALLEL H5_HAVE_ROS3_VFD H5_DOXYGEN H5_HAVE_SUBFILING_VFD H5_HAVE_IOC_VFD H5_HAVE_MIRROR_VFD'
 
   DX_INIT_DOXYGEN([HDF5], [./doxygen/Doxyfile], [hdf5lib_docs])
 fi

doxygen/CMakeLists.txt

@@ -29,7 +29,7 @@ if (DOXYGEN_FOUND)
   set (DOXYGEN_SEARCHENGINE_URL)
   set (DOXYGEN_STRIP_FROM_PATH ${HDF5_SOURCE_DIR})
   set (DOXYGEN_STRIP_FROM_INC_PATH ${HDF5_SOURCE_DIR})
-  set (DOXYGEN_PREDEFINED "H5_HAVE_DIRECT H5_HAVE_LIBHDFS H5_HAVE_MAP_API H5_HAVE_PARALLEL H5_HAVE_ROS3_VFD H5_DOXYGEN_FORTRAN")
+  set (DOXYGEN_PREDEFINED "H5_HAVE_DIRECT H5_HAVE_LIBHDFS H5_HAVE_MAP_API H5_HAVE_PARALLEL H5_HAVE_ROS3_VFD H5_DOXYGEN H5_HAVE_SUBFILING_VFD H5_HAVE_IOC_VFD H5_HAVE_MIRROR_VFD")
 
 # This configure and individual custom targets work together
   # Replace variables inside @@ with the current values

doxygen/aliases

@@ -15,7 +15,7 @@ ALIASES += Code{1}="<tt>\1</tt>"
 ALIASES += success{1}="\Bold{Success:} \1"
 ALIASES += failure{1}="\Bold{Failure:} \1"
 
-ALIASES += herr_t="Returns a non-negative value if successful; otherwise returns a negative value."
+ALIASES += herr_t="Returns a non-negative value if successful; otherwise, returns a negative value."
 ALIASES += herr_t_iter="\li Zero causes the iterator to continue, returning zero when the iteration is complete. \li A positive value causes the iterator to immediately return that positive value, indicating short-circuit success. \li A negative value causes the iterator to immediately return that value, indicating failure."
 ALIASES += hid_t{1}="Returns a \1 identifier if successful; otherwise returns #H5I_INVALID_HID. "
 ALIASES += hid_ti{1}="Returns an \1 identifier if successful; otherwise returns #H5I_INVALID_HID. "
@@ -74,7 +74,7 @@ ALIASES += space_id="\param[in] space_id Dataspace identifier"
 ALIASES += space_id{1}="\param[in] \1 Dataspace identifier"
 
 ################################################################################
-# Dataypes
+# Datatypes
 ################################################################################
 
 ALIASES += type_id="\param[in] type_id Datatype identifier"

doxygen/dox/LearnBasics2.dox

@@ -788,7 +788,7 @@ The function #H5Tarray_create creates a new array datatype object. Parameters sp
 \li the dimension permutation of the array, i.e., whether the elements of the array are listed in C or FORTRAN order.
 
 <h4>Working with existing array datatypes</h4>
-When working with existing arrays, one must first determine the the rank, or number of dimensions, of the array.
+When working with existing arrays, one must first determine the rank, or number of dimensions, of the array.
 
 The function #H5Tget_array_dims returns the rank of a specified array datatype.
 

doxygen/dox/LearnBasics3.dox

@@ -210,7 +210,7 @@ For details on compiling an HDF5 application:
 an extendible array dataset, pass in #H5P_DATASET_CREATE for the property list class.
 \li The #H5Pset_chunk call modifies a Dataset Creation Property List instance to store a chunked
 layout dataset and sets the size of the chunks used.
-\li To extend an unlimited dimension dataset use the the #H5Dset_extent call. Please be aware that
+\li To extend an unlimited dimension dataset use the #H5Dset_extent call. Please be aware that
 after this call, the dataset's dataspace must be refreshed with #H5Dget_space before more data can be accessed.
 \li The #H5Pget_chunk call retrieves the size of chunks for the raw data of a chunked layout dataset.
 \li Once there is no longer a need for a Property List instance, it should be closed with the #H5Pclose call.

doxygen/dox/Overview.dox

@@ -23,8 +23,9 @@ documents cover a mix of tasks, concepts, and reference, to help a specific
 \par Versions
      Version-specific documentation (see the version in the title area) can be found
      here:
-     - HDF5 <code>1.12</code> branch (this site)
+     - <a href="https://docs.hdfgroup.org/hdf5/develop/index.html">HDF5 <code>develop</code> branch</a>
      - <a href="https://docs.hdfgroup.org/hdf5/v1_14/index.html">HDF5 1.14.x</a>
+     - <a href="https://docs.hdfgroup.org/hdf5/v1_12/index.html">HDF5 1.12.x (this site)</a>
      - <a href="https://docs.hdfgroup.org/hdf5/v1_10/index.html">HDF5 1.10.x</a>
      - <a href="https://docs.hdfgroup.org/hdf5/v1_8/index.html">HDF5 1.8.x</a>
 

doxygen/dox/ReferenceManual.dox

@@ -158,7 +158,7 @@ Follow these simple rules and stay out of trouble:
 \li \Bold{Dynamic memory allocation:} The API contains a few functions in which the
     HDF5 library dynamically allocates memory on the caller's behalf. The caller owns
     this memory and eventually must free it by calling H5free_memory() and not language-explicit memory functions.
-\li \Bold{Be careful with that saw:} Do not modify the underlying collection when an
+\li \Bold{Don't modify while iterating:} Do not modify the underlying collection when an
     iteration is in progress!
 \li \Bold{Use of locations:} Certain API functions, typically called \Code{H5***_by_name}
     use a combination of identifiers and path names to refer to HDF5 objects.

doxygen/dox/ViewTools.dox

@@ -465,7 +465,7 @@ example <code style="background-color:whitesmoke;">h5_crtgrpar.c</code>. To disp
 \endcode
 
 \subsubsection subsubsecViewToolsViewDset_h5dumpEx5 Example 5
-The <code style="background-color:whitesmoke;">-p</code> option is used to examine the the dataset filters, storage layout, and fill value properties of a dataset.
+The <code style="background-color:whitesmoke;">-p</code> option is used to examine the dataset filters, storage layout, and fill value properties of a dataset.
 
 This option can be useful for checking how well compression works, or even for analyzing performance
 and dataset size issues related to chunking. (The smaller the chunk size, the more chunks that HDF5

doxygen/examples/H5.format.1.0.html

@@ -1488,7 +1488,7 @@ <h3><a name="GlobalHeap">Disk Format: Level 1E - Global Heap</a></h3>
 		</tr>
 
 		<tr valign=top>
-		  <td>Object Size</td> <td>This is the size of the the fields
+		  <td>Object Size</td> <td>This is the size of the fields
 		    above plus the object data stored for the object.  The
 		    actual storage size is rounded up to a multiple of
 		    eight.</td>

doxygen/examples/H5.format.1.1.html

@@ -6091,7 +6091,7 @@ <h4><a name="SharedMessage">Name: Shared Object Message</a></h4>
 		<td>Used by the library before version 1.6.1.  In this version,
 		  the Flags field is used to indicate whether the actual message is
 		  stored in the global heap (never implemented).  The Pointer field
-		  either contains the the header message address in the global heap
+		  either contains the header message address in the global heap
 		  (never implemented) or the address of the shared object header.</td>
 	      </tr>
 	    </table>

doxygen/examples/H5Pget_metadata_read_attempts.2.c

@@ -1,7 +1,7 @@
 /* Open the file with SWMR access and default file access property list */
 fid = H5Fopen(FILE, (H5F_ACC_RDONLY | H5F_ACC_SWMR_READ), H5P_DEFAULT);
 
-/* Get the file's file access roperty list */
+/* Get the file's file access property list */
 file_fapl = H5Fget_access_plist(fid);
 
 /* Retrieve the # of read attempts from the file's file access property list */
@@ -26,7 +26,7 @@ H5Pset_metadata_read_attempts(fapl, 20);
 /* Open the file with SWMR access and the non-default file access property list */
 fid = H5Fopen(FILE, (H5F_ACC_RDONLY | H5F_ACC_SWMR_READ), fapl);
 
-/* Get the file's file access roperty list */
+/* Get the file's file access property list */
 file_fapl = H5Fget_access_plist(fid);
 
 /* Retrieve the # of read attempts from the file's file access property list */

doxygen/examples/H5Pget_metadata_read_attempts.3.c

@@ -1,7 +1,7 @@
 /* Open the file with non-SWMR access and default file access property list */
 fid = H5Fopen(FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
 
-/* Get the file's file access roperty list */
+/* Get the file's file access property list */
 file_fapl = H5Fget_access_plist(fid);
 
 /* Retrieve the # of read attempts from the file's file access property list */
@@ -26,7 +26,7 @@ H5Pset_metadata_read_attempts(fapl, 20);
 /* Open the file with non-SWMR access and the non-default file access property list */
 fid = H5Fopen(FILE, H5F_ACC_RDONLY, fapl);
 
-/* Get the file's file access roperty list */
+/* Get the file's file access property list */
 file_fapl = H5Fget_access_plist(fid);
 
 /* Retrieve the # of read attempts from the file's file access property list */

doxygen/examples/H5Pset_metadata_read_attempts.c

@@ -8,7 +8,7 @@ H5Pset_metadata_read_attempts(fapl, 20);
 /* Open the file with SWMR access and the non-default file access property list */
 fid = H5Fopen(FILE, (H5F_ACC_RDONLY | H5F_ACC_SWMR_READ), fapl);
 
-/* Get the file's file access roperty list */
+/* Get the file's file access property list */
 file_fapl = H5Fget_access_plist(fid);
 
 /* Retrieve the # of read attempts from the file's file access property list */
@@ -38,7 +38,7 @@ H5Pset_metadata_read_attempts(fapl, 20);
 /* Open the file with SWMR access and the non-default file access property list */
 fid = H5Fopen(FILE, H5F_ACC_RDONLY, fapl);
 
-/* Get the file's file access roperty list */
+/* Get the file's file access property list */
 file_fapl = H5Fget_access_plist(fid);
 
 /* Retrieve the # of read attempts from the file's file access property list */

doxygen/examples/ImageSpec.html

@@ -851,31 +851,31 @@ <h3>
 "RGB"</dt>
 
 <dd>
-Each color index contains a triplet where the the first value defines the
+Each color index contains a triplet where the first value defines the
 red component, second defines the green component, and the third the blue
 component.</dd>
 
 <dt>
 "CMY"</dt>
 
 <dd>
-Each color index contains a triplet where the the first value defines the
+Each color index contains a triplet where the first value defines the
 cyan component, second defines the magenta component, and the third the
 yellow component.</dd>
 
 <dt>
 "CMYK"</dt>
 
 <dd>
-Each color index contains a quadruplet where the the first value defines
+Each color index contains a quadruplet where the first value defines
 the cyan component, second defines the magenta component, the third the
 yellow component, and the forth the black component.</dd>
 
 <dt>
 "YCbCr"</dt>
 
 <dd>
-Class Y encoding model. Each color index contains a triplet where the the
+Class Y encoding model. Each color index contains a triplet where the
 first value defines the luminance, second defines the Cb Chromonance, and
 the third the Cr Chromonance.</dd>
 
@@ -884,14 +884,14 @@ <h3>
 
 <dd>
 Composite encoding color model. Each color index contains a triplet where
-the the first value defines the luminance component, second defines the
+the first value defines the luminance component, second defines the
 chromonance component, and the third the value component.</dd>
 
 <dt>
 "HSV"</dt>
 
 <dd>
-Each color index contains a triplet where the the first value defines the
+Each color index contains a triplet where the first value defines the
 hue component, second defines the saturation component, and the third the
 value component. The hue component defines the hue spectrum with a low
 value representing magenta/red progressing to a high value which would

doxygen/examples/tables/propertyLists.dox

@@ -245,7 +245,7 @@ file access property list.</td>
 </tr>
 <tr>
 <td>#H5Pset_page_buffer_size/#H5Pget_page_buffer_size</td>
-<td>Set/get the the maximum size for the page buffer.</td>
+<td>Set/get the maximum size for the page buffer.</td>
 </tr>
 <tr>
 <td>#H5Pset_sieve_buf_size/#H5Pget_sieve_buf_size</td>
@@ -742,7 +742,7 @@ C function is a macro: \see \ref api-compat-macros.</td>
 <td>Sets up use of the Fletcher32 checksum filter.</td>
 </tr>
 <tr>
-<td>#H5Pset_local_heap_size_hint#H5Pget_local_heap_size_hint/</td>
+<td>#H5Pset_local_heap_size_hint/#H5Pget_local_heap_size_hint</td>
 <td>Sets/gets the anticipated maximum size of a local heap.</td>
 </tr>
 <tr>

doxygen/hdf5_navtree_hacks.js

@@ -141,7 +141,7 @@ function initNavTree(toroot,relpath)
   $(window).on("load", showRoot);
 }
 
-// return false if the the node has no children at all, or has only section/subsection children
+// return false if the node has no children at all, or has only section/subsection children
 function checkChildrenData(node) {
   if (!(typeof(node.childrenData)==='string')) {
     for (var i in node.childrenData) {