Hdf5 1 12 doxygen merge (#615)

* OESS-98 fix tools test for plugins

* sync fork

* Merge of changes from dev

* Move problem option to bottom of the list until fixed

* HDFFV-11106 - fix parsing optional args

* HDFFV-11106 add note

* grammer fix

* Whitespace after clang formatting

* Undo format version 11 changes

* Update check to working version

* Merge workflow and minor changes from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge serval small changes from dev

* fix typo

* Minor non-space formatting changes

* GH #386 copyright corrections for java folder

* revert because logic requires false return

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Remove case statement for H5I_EVENTSET

* Correct call with versioning

* Remove tabs

* Double underscore change

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
Remove more underscores from header guards

* Merge #380 from develop

* Correct date entry

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* Some Javadoc warning fixes

* Committing clang-format changes

* Updated javadoc fixes

* HDFFV-11228/9 merges from develop

* remove obsolete debug comment

* Fix conflict

* HDFFV-11229 merge changes from develop

* HDFFV-11229 merge second compare from develop

* HDFFV-11229 fix reference file

* 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

* Update with changes from develop

* 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.

* Whitespace changes

* Rework CMake add_custom to use the BYPRODUCTS argument

* Revert CMake configure checks for round defines

* With VS 2015 minimum strdup is supported

* Doxygen comments merged from develop

* doxygen build updates

* Correct version string for map functions

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

1 files changed, 57 insertions, 52 deletions

diff --git a/src/H5Tpublic.h b/src/H5Tpublic.h
index a6a1ef2..b708506 100644
--- a/src/H5Tpublic.h
+++ b/src/H5Tpublic.h
@@ -28,7 +28,7 @@
  * internal If this goes over 16 types (0-15), the file format will need to
  *          change.
  */
-//! [H5T_class_t_snip]
+//! <!-- [H5T_class_t_snip] -->
 typedef enum H5T_class_t {
     H5T_NO_CLASS  = -1, /**< error                                   */
     H5T_INTEGER   = 0,  /**< integer types                           */
@@ -45,12 +45,12 @@ typedef enum H5T_class_t {
 
     H5T_NCLASSES /**< sentinel: this must be last             */
 } H5T_class_t;
-//! [H5T_class_t_snip]
+//! <!-- [H5T_class_t_snip] -->
 
 /**
  * Byte orders
  */
-//! [H5T_order_t_snip]
+//! <!-- [H5T_order_t_snip] -->
 typedef enum H5T_order_t {
     H5T_ORDER_ERROR = -1, /**< error                                   */
     H5T_ORDER_LE    = 0,  /**< little endian                           */
@@ -60,12 +60,12 @@ typedef enum H5T_order_t {
     H5T_ORDER_NONE  = 4   /**< no particular order (strings, bits,..)  */
     /*H5T_ORDER_NONE must be last */
 } H5T_order_t;
-//! [H5T_order_t_snip]
+//! <!-- [H5T_order_t_snip] -->
 
 /**
  * Types of integer sign schemes
  */
-//! [H5T_sign_t_snip]
+//! <!-- [H5T_sign_t_snip] -->
 typedef enum H5T_sign_t {
     H5T_SGN_ERROR = -1, /**< error                                   */
     H5T_SGN_NONE  = 0,  /**< this is an unsigned type                */
@@ -73,12 +73,12 @@ typedef enum H5T_sign_t {
 
     H5T_NSGN = 2 /** sentinel: this must be last!             */
 } H5T_sign_t;
-//! [H5T_sign_t_snip]
+//! <!-- [H5T_sign_t_snip] -->
 
 /**
  * Floating-point normalization schemes
  */
-//! [H5T_norm_t_snip]
+//! <!-- [H5T_norm_t_snip] -->
 typedef enum H5T_norm_t {
     H5T_NORM_ERROR   = -1, /**< error                                   */
     H5T_NORM_IMPLIED = 0,  /**< msb of mantissa isn't stored, always 1  */
@@ -86,7 +86,7 @@ typedef enum H5T_norm_t {
     H5T_NORM_NONE    = 2   /**< not normalized                          */
     /*H5T_NORM_NONE must be last */
 } H5T_norm_t;
-//! [H5T_norm_t_snip]
+//! <!-- [H5T_norm_t_snip] -->
 
 /**
  * Character set to use for text strings.
@@ -141,7 +141,7 @@ typedef enum H5T_str_t {
 /**
  * Type of padding to use in other atomic types
  */
-//! [H5T_pad_t_snip]
+//! <!-- [H5T_pad_t_snip] -->
 typedef enum H5T_pad_t {
     H5T_PAD_ERROR      = -1, /**< error                           */
     H5T_PAD_ZERO       = 0,  /**< always set to zero              */
@@ -150,7 +150,7 @@ typedef enum H5T_pad_t {
 
     H5T_NPAD = 3 /**< sentinal: THIS MUST BE LAST     */
 } H5T_pad_t;
-//! [H5T_pad_t_snip]
+//! <!-- [H5T_pad_t_snip] -->
 
 /**
  * Commands sent to conversion functions
@@ -173,14 +173,14 @@ typedef enum H5T_bkg_t {
 /**
  * Type conversion client data
  */
-//! [H5T_cdata_t_snip]
+//! <!-- [H5T_cdata_t_snip] -->
 typedef struct H5T_cdata_t {
     H5T_cmd_t command;  /**< what should the conversion function do?    */
     H5T_bkg_t need_bkg; /**< is the background buffer needed?	     */
     hbool_t   recalc;   /**< recalculate private data		     */
     void *    priv;     /**< private data				     */
 } H5T_cdata_t;
-//! [H5T_cdata_t_snip]
+//! <!-- [H5T_cdata_t_snip] -->
 
 /**
  * Conversion function persistence
@@ -194,25 +194,32 @@ typedef enum H5T_pers_t {
 /**
  * The order to retrieve atomic native datatype
  */
-//! [H5T_direction_t_snip]
+//! <!-- [H5T_direction_t_snip] -->
 typedef enum H5T_direction_t {
     H5T_DIR_DEFAULT = 0, /**< default direction is inscendent        */
     H5T_DIR_ASCEND  = 1, /**< in inscendent order                    */
     H5T_DIR_DESCEND = 2  /**< in descendent order                    */
 } H5T_direction_t;
-//! [H5T_direction_t_snip]
+//! <!-- [H5T_direction_t_snip] -->
 
 /**
  * The exception type passed into the conversion callback function
  */
 typedef enum H5T_conv_except_t {
-    H5T_CONV_EXCEPT_RANGE_HI  = 0, /**< source value is greater than destination's range */
-    H5T_CONV_EXCEPT_RANGE_LOW = 1, /**< source value is less than destination's range    */
-    H5T_CONV_EXCEPT_PRECISION = 2, /**< source value loses precision in destination      */
-    H5T_CONV_EXCEPT_TRUNCATE  = 3, /**< source value is truncated in destination         */
-    H5T_CONV_EXCEPT_PINF      = 4, /**< source value is positive infinity(floating number) */
-    H5T_CONV_EXCEPT_NINF      = 5, /**< source value is negative infinity(floating number) */
-    H5T_CONV_EXCEPT_NAN       = 6  /**< source value is NaN(floating number)             */
+    H5T_CONV_EXCEPT_RANGE_HI = 0,
+    /**< Source value is greater than destination's range */
+    H5T_CONV_EXCEPT_RANGE_LOW = 1,
+    /**< Source value is less than destination's range */
+    H5T_CONV_EXCEPT_PRECISION = 2,
+    /**< Source value loses precision in destination */
+    H5T_CONV_EXCEPT_TRUNCATE = 3,
+    /**< Source value is truncated in destination */
+    H5T_CONV_EXCEPT_PINF = 4,
+    /**< Source value is positive infinity */
+    H5T_CONV_EXCEPT_NINF = 5,
+    /**< Source value is negative infinity */
+    H5T_CONV_EXCEPT_NAN = 6
+    /**< Source value is \c NaN (not a number, including \c QNaN and \c SNaN) */
 } H5T_conv_except_t;
 
 /**
@@ -254,17 +261,31 @@ extern "C" {
 /**
  * All datatype conversion functions are...
  */
-//! [H5T_conv_t_snip]
+//! <!-- [H5T_conv_t_snip] -->
 typedef herr_t (*H5T_conv_t)(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts, size_t buf_stride,
                              size_t bkg_stride, void *buf, void *bkg, hid_t dset_xfer_plist);
-//! [H5T_conv_t_snip]
+//! <!-- [H5T_conv_t_snip] -->
 
+//! <!-- [H5T_conv_except_func_t_snip] -->
 /**
- * Exception handler.  If an exception like overflow happenes during conversion,
- * this function is called if it's registered through H5Pset_type_conv_cb().
+ * \brief Exception handler.
+ *
+ * \param[in] except_type The kind of exception that occurred
+ * \param[in] src_id Source datatype identifier
+ * \param[in] dst_id Destination datatype identifier
+ * \param[in] src_buf Source data buffer
+ * \param[in,out] dst_buf Destination data buffer
+ * \param[in,out] user_data Callback context
+ * \returns Valid callback function return values are #H5T_CONV_ABORT,
+ *          #H5T_CONV_UNHANDLED and #H5T_CONV_HANDLED.
+ *
+ * \details If an exception like overflow happenes during conversion, this
+ *          function is called if it's registered through H5Pset_type_conv_cb().
+ *
  */
 typedef H5T_conv_ret_t (*H5T_conv_except_func_t)(H5T_conv_except_t except_type, hid_t src_id, hid_t dst_id,
                                                  void *src_buf, void *dst_buf, void *user_data);
+//! <!-- [H5T_conv_except_func_t_snip] -->
 
 /* When this header is included from a private header, don't make calls to H5open() */
 #undef H5OPEN
@@ -1061,7 +1082,7 @@ H5_DLLVAR hid_t H5T_NATIVE_UINT_FAST64_g;
  *          predefined datatype.
  *
  *          When creating a variable-length string datatype, \p size must
- *          be #H5T_VARIABLE.
+ *          be #H5T_VARIABLE; see \ref_vlen_strings.
  *
  *          When creating a fixed-length string datatype, \p size will
  *          be the length of the string in bytes. The length of the
@@ -1075,13 +1096,9 @@ H5_DLLVAR hid_t H5T_NATIVE_UINT_FAST64_g;
  *          The datatype identifier returned from this function should be
  *          released with H5Tclose or resource leaks will result.
  *
- * \since 1.2.0
- *
  * \see H5Tclose()
  *
- * \todo Original has a reference to “Creating variable-length string
- *       datatypes”.
- * \todo Create an example for H5Tcreate.
+ * \since 1.2.0
  *
  */
 H5_DLL hid_t H5Tcreate(H5T_class_t type, size_t size);
@@ -1106,8 +1123,6 @@ H5_DLL hid_t H5Tcreate(H5T_class_t type, size_t size);
  *          The returned datatype identifier should be released with H5Tclose()
  *          to prevent resource leak.
  *
- * \todo Create an example for H5Tcopy().
- *
  */
 H5_DLL hid_t H5Tcopy(hid_t type_id);
 /**
@@ -1472,8 +1487,6 @@ H5_DLL herr_t H5Trefresh(hid_t type_id);
  *
  * \since 1.2.0
  *
- * \todo Create example for  H5Tinsert
- *
  */
 H5_DLL herr_t H5Tinsert(hid_t parent_id, const char *name, size_t offset, hid_t member_id);
 /**
@@ -1632,10 +1645,7 @@ H5_DLL herr_t H5Tenum_valueof(hid_t type, const char *name, void *value /*out*/)
  *            character base type creates a variable-length sequence of strings
  *            (a variable-length, 1-dimensional array), with each element of
  *            the array being of the string or character base type.\n
- *            To create a variable-length string datatype, see "Creating
- *            variable-length string datatypes."
- *
- * \todo Fix the reference.
+ *            To create a variable-length string datatype, see \ref_vlen_strings.
  *
  */
 H5_DLL hid_t H5Tvlen_create(hid_t base_id);
@@ -1839,13 +1849,9 @@ H5_DLL htri_t H5Tdetect_class(hid_t type_id, H5T_class_t cls);
  *          actual data and a size value.  This function does not return the
  *          size of actual variable-length sequence data.
  *
- * \since 1.2.0
- *
  * \see H5Tset_size()
  *
- * \todo Original has a reference to “Creating variable-length string datatypes”.
- * \todo Create an example for H5Tget_size().
- *
+ * \since 1.2.0
  */
 H5_DLL size_t H5Tget_size(hid_t type_id);
 /**
@@ -2059,7 +2065,7 @@ H5_DLL H5T_pad_t H5Tget_inpad(hid_t type_id);
  */
 H5_DLL H5T_str_t H5Tget_strpad(hid_t type_id);
 /**
- * \ingroup COMPOUND
+ * \ingroup COMPOUND ENUM
  *
  * \brief Retrieves the number of elements in a compound or enumeration datatype
  *
@@ -2076,7 +2082,7 @@ H5_DLL H5T_str_t H5Tget_strpad(hid_t type_id);
  */
 H5_DLL int H5Tget_nmembers(hid_t type_id);
 /**
- * \ingroup COMPOUND
+ * \ingroup COMPOUND ENUM
  *
  * \brief Retrieves the name of a compound or enumeration datatype member
  *
@@ -2103,7 +2109,7 @@ H5_DLL int H5Tget_nmembers(hid_t type_id);
  */
 H5_DLL char *H5Tget_member_name(hid_t type_id, unsigned membno);
 /**
- * \ingroup COMPOUND
+ * \ingroup COMPOUND ENUM
  *
  * \brief Retrieves the index of a compound or enumeration datatype member
  *
@@ -2375,6 +2381,7 @@ H5_DLL hid_t H5Tget_native_type(hid_t type_id, H5T_direction_t direction);
  *
  *          \li Variable-length string datatypes: If \p dtype_id is a
  *          variable-length string, size must normally be set to #H5T_VARIABLE.
+ *          See \ref_vlen_strings.
  *
  *          \li Compound datatypes: This function may be used to increase or
  *          decrease the size of a compound datatype, but the function will
@@ -2385,12 +2392,9 @@ H5_DLL hid_t H5Tget_native_type(hid_t type_id, H5T_direction_t direction);
  *          variable-length array datatypes (#H5T_VLEN), or reference datatypes
  *          (#H5T_REFERENCE).
  *
- * \since 1.2.0
- *
  * \see H5Tget_size()
  *
- *\todo Create an example for H5Tset_size().
- *\todo Original has a reference to “Creating variable-length string datatypes”.
+ * \since 1.2.0
  *
  */
 H5_DLL herr_t H5Tset_size(hid_t type_id, size_t size);
@@ -2842,7 +2846,7 @@ H5_DLL htri_t H5Tcompiler_conv(hid_t src_id, hid_t dst_id);
  *       enough to hold the larger of the input and output data.
  *
  * \version 1.6.3 \p nelmts parameter type changed to size_t.
- * \version 1.4.0 \p nelmts parameter type changed to \ref hsize_t.
+ * \version 1.4.0 \p nelmts parameter type changed to hsize_t.
  *
  */
 H5_DLL herr_t H5Tconvert(hid_t src_id, hid_t dst_id, size_t nelmts, void *buf, void *background,
@@ -2875,6 +2879,7 @@ H5_DLL herr_t H5Treclaim(hid_t type_id, hid_t space_id, hid_t plist_id, void *bu
  *
  * Use of these symbols is deprecated.
  */
+
 #ifndef H5_NO_DEPRECATED_SYMBOLS
 
 /* Macros */