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, 342 insertions, 14 deletions

diff --git a/src/H5Rpublic.h b/src/H5Rpublic.h
index 1fc41ec..348a7a2 100644
--- a/src/H5Rpublic.h
+++ b/src/H5Rpublic.h
@@ -42,26 +42,39 @@
 /* Public Typedefs */
 /*******************/
 
-/* Reference types */
-typedef enum H5R_type_t {
-    H5R_BADTYPE = (-1), /* Invalid Reference Type               */
-    H5R_OBJECT,         /* Object reference                     */
-    H5R_DATASET_REGION, /* Dataset Region Reference             */
-    H5R_MAXTYPE         /* Highest type (Invalid as true type)  */
+//! <!-- [H5R_type_t_snip] -->
+/**
+ * Reference types allowed.
+ *
+ * \internal DO NOT CHANGE THE ORDER or VALUES as reference type values are
+ *           encoded into the datatype message header.
+ */
+typedef enum {
+    H5R_BADTYPE = (-1), /**< Invalid reference type               */
+    H5R_OBJECT,         /**< Object reference                     */
+    H5R_DATASET_REGION, /**< Dataset Region Reference             */
+    H5R_MAXTYPE         /**< Highest type (Invalid as true type)  */
 } H5R_type_t;
+//! <!-- [H5R_type_t_snip] -->
 
-/* Object reference structure for user's code
+//! <!-- [hobj_ref_t_snip] -->
+/**
+ * Object reference structure for user's code
  * This needs to be large enough to store largest haddr_t on a worst case
  * machine (8 bytes currently).
  */
 typedef haddr_t hobj_ref_t;
+//! <!-- [hobj_ref_t_snip] -->
 
-/* Dataset Region reference structure for user's code
+//! <!-- [hdset_reg_ref_t_snip] -->
+/**
+ * Dataset Region reference structure for user's code
  * (Buffer to store heap ID and index)
  * This needs to be large enough to store largest haddr_t in a worst case
  * machine (8 bytes currently) plus an int
  */
 typedef unsigned char hdset_reg_ref_t[H5R_DSET_REG_REF_BUF_SIZE];
+//! <!-- [hdset_reg_ref_t_snip] -->
 
 /********************/
 /* Public Variables */
@@ -75,10 +88,223 @@ typedef unsigned char hdset_reg_ref_t[H5R_DSET_REG_REF_BUF_SIZE];
 extern "C" {
 #endif
 
-H5_DLL herr_t  H5Rcreate(void *ref, hid_t loc_id, const char *name, H5R_type_t ref_type, hid_t space_id);
-H5_DLL hid_t   H5Rdereference2(hid_t obj_id, hid_t oapl_id, H5R_type_t ref_type, const void *ref);
-H5_DLL hid_t   H5Rget_region(hid_t dataset, H5R_type_t ref_type, const void *ref);
-H5_DLL herr_t  H5Rget_obj_type2(hid_t id, H5R_type_t ref_type, const void *_ref, H5O_type_t *obj_type);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5R
+ *
+ * \brief Creates a reference
+ *
+ * \param[out] ref Reference created by the function call
+ * \param[in] loc_id Location identifier used to locate the object being pointed to
+ * \param[in] name Name of object at location \p loc_id
+ * \param[in] ref_type Type of reference
+ * \param[in] space_id Dataspace identifier with selection. Used only for
+ *                     dataset region references; pass as -1 if reference is
+ *                     an object reference, i.e., of type #H5R_OBJECT
+ *
+ * \return \herr_t
+ *
+ * \details H5Rcreate() creates the reference, \p ref, of the type specified in
+ *          \p ref_type, pointing to the object \p name located at \p loc_id.
+ *
+ *          The HDF5 library maps the void type specified above for \p ref to
+ *          the type specified in \p ref_type, which will be one of the following:
+ *          \snippet this H5R_type_t_snip
+ *
+ *          The parameters \p loc_id and \p name are used to locate the object.
+ *
+ *          The parameter \p space_id identifies the dataset region that a
+ *          dataset region reference points to. This parameter is used only with
+ *          dataset region references and should be set to -1 if the reference
+ *          is an object reference, #H5R_OBJECT.
+ *
+ * \since 1.8.0
+ */
+H5_DLL herr_t H5Rcreate(void *ref, hid_t loc_id, const char *name, H5R_type_t ref_type, hid_t space_id);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5R
+ *
+ * \brief Opens the HDF5 object referenced
+ *
+ * \obj_id
+ * \oapl_id
+ * \param[in] ref_type The reference type of \p ref
+ * \param[in] ref Reference to open
+ *
+ * \return Returns identifier of referenced object if successful; otherwise
+ *         returns a negative value.
+ *
+ * \details Given a reference, \p ref, to an object or a region in an object,
+ *          H5Rdereference2() opens that object and returns an identifier.
+ *
+ *          The parameter \p obj_id must be a valid identifier for the HDF5 file
+ *          containing the referenced object or for any object in that HDF5
+ *          file.
+ *
+ *          The parameter \p oapl_id is an object access property list
+ *          identifier for the referenced object. The access property list must
+ *          be of the same type as the object being referenced, that is a group,
+ *          dataset, or datatype property list.
+ *
+ *          The parameter \p ref_type specifies the reference type of the
+ *          reference \p ref. \p ref_type may contain either of the following
+ *          values:
+ *          - #H5R_OBJECT
+ *          - #H5R_DATASET_REGION
+ *
+ *          The object opened with this function should be closed when it is no
+ *          longer needed so that resource leaks will not develop. Use the
+ *          appropriate close function such as H5Oclose() or H5Dclose() for
+ *          datasets.
+ *
+ * \since 1.10.0
+ *
+ */
+H5_DLL hid_t H5Rdereference2(hid_t obj_id, hid_t oapl_id, H5R_type_t ref_type, const void *ref);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5R
+ *
+ * \brief Sets up a dataspace and selection as specified by a region reference
+ *
+ * \param[in] dataset File identifier or identifier for any object in the file
+ *                    containing the referenced region
+ * \param[in] ref_type Reference type of \p ref, which must be #H5R_DATASET_REGION
+ * \param[in] ref Region reference to open
+ *
+ * \return Returns a valid dataspace identifier if successful; otherwise returns
+ *         a negative value.
+ *
+ * \details H5Rget_region() creates a copy of the dataspace of the dataset
+ *          pointed to by a region reference, \p ref, and defines a selection
+ *          matching the selection pointed to by ref within the dataspace copy.
+ *
+ *          \p dataset is used to identify the file containing the referenced
+ *          region; it can be a file identifier or an identifier for any object
+ *          in the file.
+ *
+ *          The parameter \p ref_type specifies the reference type of \p ref and
+ *          must contain the value #H5R_DATASET_REGION.
+ *
+ *          Use H5Sclose() to release the dataspace identifier returned by this
+ *          function when the identifier is no longer needed.
+ *
+ */
+H5_DLL hid_t H5Rget_region(hid_t dataset, H5R_type_t ref_type, const void *ref);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5R
+ *
+ * \brief Retrieves the type of object that an object reference points to
+ *
+ * \param[in] id The dataset containing the reference object or the group
+ *            containing that dataset
+ * \param[in] ref_type Type of reference to query
+ * \param[in] ref Reference to query
+ * \param[out] obj_type Type of referenced object
+ *
+ * \return \herr_t
+ *
+ * \details Given an object reference, \p ref, H5Rget_obj_type2() returns the
+ *          type of the referenced object in \p obj_type.
+ *
+ *          A \Emph{reference type} is the type of reference, either an object
+ *          reference or a dataset region reference. An \Emph{object reference}
+ *          points to an HDF5 object while a \Emph{dataset region reference}
+ *          points to a defined region within a dataset.
+ *
+ *          The \Emph{referenced object} is the object the reference points
+ *          to. The \Emph{referenced object type}, or the type of the referenced
+ *          object, is the type of the object that the reference points to.
+ *
+ *          The location identifier, \p id, is the identifier for either the
+ *          dataset containing the object reference or the group containing that
+ *          dataset.
+ *
+ *          Valid reference types, to pass in as \p ref_type, include the
+ *          following:
+ *          \snippet this H5R_type_t_snip
+ *
+ *          If the application does not already know the object reference type,
+ *          that can be determined with three preliminary calls:
+ *
+ *          \li Call H5Dget_type() on the dataset containing the reference to
+ *              get a datatype identifier for the dataset’s datatype.
+ *          \li Using that datatype identifier, H5Tget_class() returns a datatype
+ *              class.\n If the datatype class is #H5T_REFERENCE, H5Tequal() can
+ *              then be used to determine whether the reference’s datatype is
+ *              #H5T_STD_REF_OBJ or #H5T_STD_REF_DSETREG:
+ *              - If the datatype is #H5T_STD_REF_OBJ, the reference object type
+ *                is #H5R_OBJECT.
+ *              - If the datatype is #H5T_STD_REF_DSETREG, the reference object
+ *                type is #H5R_DATASET_REGION.
+ *
+ *          When the function completes successfully, it returns one of the
+ *          following valid object type values (defined in H5Opublic.h):
+ *          \snippet H5Opublic.h H5O_type_t_snip
+ *
+ * \since 1.8.0
+ *
+ */
+H5_DLL herr_t H5Rget_obj_type2(hid_t id, H5R_type_t ref_type, const void *_ref, H5O_type_t *obj_type);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5R
+ *
+ * \brief Retrieves a name for a referenced object
+ *
+ * \param[in] loc_id Identifier for the file containing the reference or for
+ *                   any object in that file
+ * \param[in] ref_type Type of reference
+ * \param[in] ref An object or dataset region reference
+ * \param[out] name A buffer to place the name of the referenced object or
+ *                  dataset region. If \c NULL, then this call will return the
+ *                  size in bytes of the name.
+ * \param[in] size The size of the \p name buffer. When the size is passed in,
+ *                 the \c NULL terminator needs to be included.
+ *
+ * \return Returns the length of the name if successful, returning 0 (zero) if
+ *         no name is associated with the identifier. Otherwise returns a
+ *         negative value.
+ *
+ * \details H5Rget_name() retrieves a name for the object identified by \p ref.\n
+ *          \p loc_id is used to identify the file containing the reference. It
+ *          can be the file identifier for the file containing the reference or
+ *          an identifier for any object in that file.
+ *
+ *          \ref H5R_type_t is the reference type of \p ref. Valid values
+ *          include the following:
+ *          \snippet this H5R_type_t_snip
+ *
+ *          \p ref is the reference for which the target object’s name is
+ *          sought.
+ *
+ *          If \p ref is an object reference, \p name will be returned with a
+ *          name for the referenced object. If \p ref is a dataset region
+ *          reference, \p name will contain a name for the object containing the
+ *          referenced region.
+ *
+ *          Up to \p size characters of the name are returned in \p name;
+ *          additional characters, if any, are not returned to the user
+ *          application.
+ *
+ *          If the length of the name, which determines the required value of \p
+ *          size, is unknown, a preliminary H5Rget_name() call can be made. The
+ *          return value of this call will be the size of the object name. That
+ *          value can then be assigned to \p size for a second H5Rget_name()
+ *          call, which will retrieve the actual name.
+ *
+ *          If there is no name associated with the object identifier or if the
+ *          \p name is \c NULL, H5Rget_name() returns the size of the \p name
+ *          buffer (the size does not include the \p NULL terminator).
+ *
+ *          Note that an object in an HDF5 file may have multiple paths if there
+ *          are multiple links pointing to it. This function may return any one
+ *          of these paths.
+ *
+ * \since 1.8.0
+ */
 H5_DLL ssize_t H5Rget_name(hid_t loc_id, H5R_type_t ref_type, const void *ref, char *name /*out*/,
                            size_t size);
 
@@ -89,8 +315,110 @@ H5_DLL ssize_t H5Rget_name(hid_t loc_id, H5R_type_t ref_type, const void *ref, c
 #ifndef H5_NO_DEPRECATED_SYMBOLS
 
 /* Function prototypes */
-H5_DLL H5G_obj_t H5Rget_obj_type1(hid_t id, H5R_type_t ref_type, const void *_ref);
-H5_DLL hid_t     H5Rdereference1(hid_t obj_id, H5R_type_t ref_type, const void *ref);
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5R
+ *
+ * \brief Retrieves the type of object that an object reference points to
+ *
+ * \param[in] id The dataset containing the reference object or the group
+ *            containing that dataset
+ * \param[in] ref_type Type of reference to query
+ * \param[in] ref Reference to query
+ *
+ * \return Returns a valid object type if successful; otherwise returns a
+ *         negative value (#H5G_UNKNOWN).
+ *
+ * \deprecated This function has been renamed from H5Rget_obj_type() and is
+ *             deprecated in favor of the macro H5Rget_obj_type() or the
+ *             function H5Rget_obj_type2().
+ *
+ * \details Given an object reference, \p ref, H5Rget_obj_type1() returns the
+ *          type of the referenced object.
+ *
+ *          A \Emph{reference type} is the type of reference, either an object
+ *          reference or a dataset region reference. An \Emph{object reference}
+ *          points to an HDF5 object while a \Emph{dataset region reference}
+ *          points to a defined region within a dataset.
+ *
+ *          The \Emph{referenced object} is the object the reference points
+ *          to. The \Emph{referenced object type}, or the type of the referenced
+ *          object, is the type of the object that the reference points to.
+ *
+ *          The location identifier, \p id, is the identifier for either the
+ *          dataset containing the object reference or the group containing that
+ *          dataset.
+ *
+ *          Valid reference types, to pass in as \p ref_type, include the
+ *          following:
+ *          \snippet this H5R_type_t_snip
+ *
+ *          If the application does not already know the object reference type,
+ *          that can be determined with three preliminary calls:
+ *
+ *          \li Call H5Dget_type() on the dataset containing the reference to
+ *              get a datatype identifier for the dataset’s datatype.
+ *          \li Using that datatype identifier, H5Tget_class() returns a datatype
+ *              class.\n If the datatype class is #H5T_REFERENCE, H5Tequal() can
+ *              then be used to determine whether the reference’s datatype is
+ *              #H5T_STD_REF_OBJ or #H5T_STD_REF_DSETREG:
+ *              - If the datatype is #H5T_STD_REF_OBJ, the reference object type
+ *                is #H5R_OBJECT.
+ *              - If the datatype is #H5T_STD_REF_DSETREG, the reference object
+ *                type is #H5R_DATASET_REGION.
+ *
+ *          When the function completes successfully, it returns one of the
+ *          following valid object type values (defined in H5Gpublic.h):
+ *          \snippet H5Gpublic.h H5G_obj_t_snip
+ *
+ * \version 1.8.0 Function H5Rget_obj_type() renamed to H5Rget_obj_type1() and
+ *                deprecated in this release.
+ * \since 1.6.0
+ *
+ */
+H5_DLL H5G_obj_t H5Rget_obj_type1(hid_t id, H5R_type_t ref_type, const void *ref);
+
+/**
+ * --------------------------------------------------------------------------
+ * \ingroup H5R
+ *
+ * \brief Opens the HDF5 object referenced
+ *
+ * \obj_id
+ * \param[in] ref_type The reference type of \p ref
+ * \param[in] ref Reference to open
+ *
+ * \return Returns identifier of referenced object if successful; otherwise
+ *         returns a negative value.
+ *
+ * \deprecated This function has been renamed from H5Rdereference() and is
+ *             deprecated in favor of the macro H5Rdereference() or the function
+ *             H5Rdereference2().
+ *
+ * \details Given a reference, \p ref, to an object or a region in an object,
+ *          H5Rdereference1() opens that object and returns an identifier.
+ *
+ *          The parameter \p obj_id must be a valid identifier for an object in
+ *          the HDF5 file containing the referenced object, including the file
+ *          identifier.
+ *
+ *          The parameter \p ref_type specifies the reference type of the
+ *          reference \p ref. \p ref_type may contain either of the following
+ *          values:
+ *          - #H5R_OBJECT
+ *          - #H5R_DATASET_REGION
+ *
+ *          The object opened with this function should be closed when it is no
+ *          longer needed so that resource leaks will not develop. Use the
+ *          appropriate close function such as H5Oclose() or H5Dclose() for
+ *          datasets.
+ *
+ * \version 1.10.0 Function H5Rdereference() renamed to H5Rdereference1() and
+ *                 deprecated in this release.
+ * \since 1.8.0
+ *
+ */
+H5_DLL hid_t H5Rdereference1(hid_t obj_id, H5R_type_t ref_type, const void *ref);
 
 #endif /* H5_NO_DEPRECATED_SYMBOLS */