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, 75 insertions, 1 deletions

diff --git a/doxygen/aliases b/doxygen/aliases
index c10c3e8..af43902 100644
--- a/doxygen/aliases
+++ b/doxygen/aliases
@@ -1,3 +1,5 @@
+ALIASES += THG="The HDF Group"
+
 ################################################################################
 # Styling
 ################################################################################
@@ -35,6 +37,15 @@ ALIASES += op{1}="\param[in] \1 Callback function"
 ALIASES += op_data="\param[in,out] op_data User-defined callback function context"
 ALIASES += op_data{1}="\param[in,out] \1 User-defined callback function context"
 
+ALIASES += op_data_in="\param[in] op_data User-defined callback function context"
+ALIASES += op_data_in{1}="\param[in] \1 User-defined callback function context"
+
+################################################################################
+# Asynchronous
+################################################################################
+
+ALIASES += async_variant_of{1}="Asynchronous version of \1()"
+
 ################################################################################
 # Attributes
 ################################################################################
@@ -67,6 +78,13 @@ ALIASES += file_type_id{1}="\param[in] \1 Datatype (in-file) identifier"
 ALIASES += mem_type_id{1}="\param[in] \1 Datatype (in-memory) identifier"
 
 ################################################################################
+# Errors
+################################################################################
+
+ALIASES += estack_id="\param[in] estack_id Error stack identifier"
+ALIASES += estack_id{1}="\param[in] \1 Error stack identifier"
+
+################################################################################
 # Files
 ################################################################################
 
@@ -103,6 +121,13 @@ ALIASES += fg_loc_id="\loc_id. The identifier may be that of a file or group."
 ALIASES += fg_loc_id{1}="\loc_id{\1}. The identifier may be that of a file or group."
 
 ################################################################################
+# Maps
+################################################################################
+
+ALIASES += map_id="\param[in] map_id Map identifier"
+ALIASES += map_id{1}="\param[in] \1 Map identifier"
+
+################################################################################
 # Property lists
 ################################################################################
 
@@ -121,6 +146,9 @@ ALIASES += dcpl_id{1}="\param[in] \1 Dataset creation property list identifier"
 ALIASES += dxpl_id="\param[in] dxpl_id Dataset transfer property list identifier"
 ALIASES += dxpl_id{1}="\param[in] \1 Dataset transfer property list identifier"
 
+ALIASES += gacpl_id="\param[in] plist_id File, group, dataset, datatype, link, or attribute access property list identifier"
+ALIASES += gacpl_id{1}="\param[in] \1 File, group, dataset, datatype, link, or attribute access property list identifier"
+
 ALIASES += gapl_id="\param[in] gapl_id Group access property list identifier"
 ALIASES += gapl_id{1}="\param[in] \1 Group access property list identifier"
 
@@ -133,12 +161,27 @@ ALIASES += lapl_id{1}="\param[in] \1 Link access property list identifier"
 ALIASES += lcpl_id="\param[in] lcpl_id Link creation property list identifier"
 ALIASES += lcpl_id{1}="\param[in] \1 Link creation property list identifier"
 
+ALIASES += mapl_id="\param[in] mapl_id Map access property list identifier"
+ALIASES += mapl_id{1}="\param[in] \1 Map access property list identifier"
+
+ALIASES += mcpl_id="\param[in] mcpl_id Map creation property list identifier"
+ALIASES += mcpl_id{1}="\param[in] \1 Map creation property list identifier"
+
+ALIASES += oapl_id="\param[in] oapl_id Object access property list identifier"
+ALIASES += oapl_id{1}="\param[in] \1 Object access property list identifier"
+
+ALIASES += ocpl_id="\param[in] oapl_id Object creation property list identifier"
+ALIASES += ocpl_id{1}="\param[in] \1 Object creation property list identifier"
+
 ALIASES += plist_id="\param[in] plist_id Property list identifier"
 ALIASES += plist_id{1}="\param[in] \1 Property list identifier"
 
 ALIASES += plistcls_id="\param[in] plistcls_id Property list class identifier"
 ALIASES += plistcls_id{1}="\param[in] \1 Property list class identifier"
 
+ALIASES += rapl_id="\param[in] rapl_id Reference access property list identifier"
+ALIASES += rapl_id{1}="\param[in] \1 Reference access property list identifier"
+
 ALIASES += tapl_id="\param[in] tapl_id Datatype access property list identifier"
 ALIASES += tapl_id{1}="\param[in] \1 Datatype access property list identifier"
 
@@ -161,16 +204,47 @@ ALIASES += fgdta_obj_id{1}="\obj_id{\1}. The identifier may be that of a file, g
 ALIASES += fgdta_loc_obj_id{1}="\loc_obj_id{\1}. The identifier may be that of a file, group, dataset, named datatype, or attribute."
 
 ################################################################################
+# Asynchronous Arguments
+################################################################################
+
+ALIASES += app_file="\param[in] app_file For internal use only, not a visible user parameter"
+ALIASES += app_func="\param[in] app_func For internal use only, not a visible user parameter"
+ALIASES += app_line="\param[in] app_line For internal use only, not a visible user parameter"
+ALIASES += es_id="\param[in] es_id Event set identifier"
+ALIASES += es_id{1}="\param[in] \1 Event set identifier"
+
+################################################################################
 # Others
 ################################################################################
 
 ALIASES += estack_id="\param[in] estack_id Error stack identifier"
 ALIASES += estack_id{1}="\param[in] \1 Error stack identifier"
+ALIASES += cpp_c_api_note="\attention \Bold{C++ Developers using HDF5 C-API functions beware:}\n Several functions in this C-API take function pointers or callbacks as arguments. Examples include H5Pset_elink_cb(), H5Pset_type_conv_cb(), H5Tconvert(), and H5Ewalk2(). Application code must ensure that those callback functions return normally such to allow the HDF5 to manage its resources and maintain a consistent state. For instance, those functions must not use the C \c setjmp / \c longjmp mechanism to leave those callback functions. Within the context of C++, any exceptions thrown within the callback function must be caught, such as with a \Code{catch(…)} statement. Any exception state can be placed within the provided user data function call arguments, and may be thrown again once the calling function has returned. Exceptions raised and not handled inside the callback are not supported as it might leave the HDF5 library in an inconsistent state. Similarly, using C++20 coroutines cannot be used as callbacks, since they do not support plain return statements. If a callback function yields execution to another C++20 coroutine calling HDF5 functions as well, this may lead to undefined behavior."
+ALIASES += sa_metadata_ops="\sa \li H5Pget_all_coll_metadata_ops() \li H5Pget_coll_metadata_write() \li H5Pset_all_coll_metadata_ops() \li H5Pset_coll_metadata_write() \li \ref maybe_metadata_reads"
+
+################################################################################
+# References
+################################################################################
+
+ALIASES += ref_cons_semantics="<a href=\"https://portal.hdfgroup.org/display/HDF5/Enabling+a+Strict+Consistency+Semantics+Model+in+Parallel+HDF5\">Enabling a Strict Consistency Semantics Model in Parallel HDF5</a>"
+ALIASES += ref_dld_filters="<a href=\"https://portal.hdfgroup.org/display/HDF5/HDF5+Dynamically+Loaded+Filters\">HDF5 Dynamically Loaded Filters</a>"
+ALIASES += ref_file_image_ops="<a href=\"https://portal.hdfgroup.org/display/HDF5/HDF5+File+Image+Operations\">HDF5 File Image Operations</a>"
+ALIASES += ref_filter_pipe="<a href=\"https://portal.hdfgroup.org/display/HDF5/HDF5+Data+Flow+Pipeline+for+H5Dread\">Data Flow Pipeline for H5Dread()</a>"
+ALIASES += ref_group_impls="<a href=\"https://portal.hdfgroup.org/display/HDF5/Groups\">Group implementations in HDF5</a>"
+ALIASES += ref_h5lib_relver="<a href=\"https://portal.hdfgroup.org/display/HDF5/HDF5+Library+Release+Version+Numbers\">HDF5 Library Release Version Numbers</a>"
+ALIASES += ref_mdc_in_hdf5="<a href=\"https://portal.hdfgroup.org/display/HDF5/Metadata+Caching+in+HDF5\">Metadata Caching in HDF5</a>"
+ALIASES += ref_mdc_logging="<a href=\"https://portal.hdfgroup.org/display/HDF5/H5F_START_MDC_LOGGING\">Metadata Cache Logging</a>"
+ALIASES += ref_news_112="<a href=\"https://portal.hdfgroup.org/display/HDF5/New+Features+in+HDF5+Release+1.12\">New Features in HDF5 Release 1.12</a>"
+ALIASES += ref_h5ocopy="<a href=\"https://portal.hdfgroup.org/display/HDF5/Copying+Committed+Datatypes+with+H5Ocopy\">Copying Committed Datatypes with H5Ocopy()</a>"
+ALIASES += ref_sencode_fmt_change="<a href=\"https://portal.hdfgroup.org/pages/viewpage.action?pageId=58100093&preview=/58100093/58100094/encode_format_RFC.pdf\">RFC H5Secnode() / H5Sdecode() Format Change</a>"
+ALIASES += ref_vlen_strings="\Emph{Creating variable-length string datatypes}"
+ALIASES += ref_vol_doc="VOL documentation"
 
 ################################################################################
 # The Usual Suspects
 ################################################################################
 
+ALIASES += click4more="(Click on a enumerator, field, or type for more information.)"
 ALIASES += csets="<table><tr><td>#H5T_CSET_ASCII</td><td>US ASCII</td></tr><tr><td>#H5T_CSET_UTF8</td><td>UTF-8 Unicode encoding</td></tr></table>"
 ALIASES += datatype_class=" \li #H5T_INTEGER \li #H5T_FLOAT \li #H5T_STRING \li #H5T_BITFIELD \li #H5T_OPAQUE \li #H5T_COMPOUND \li #H5T_REFERENCE \li #H5T_ENUM \li #H5T_VLEN \li #H5T_ARRAY"
 ALIASES += file_access="<table><tr><td>#H5F_ACC_RDWR</td><td>File was opened with read/write access.</td></tr><tr><td>#H5F_ACC_RDONLY</td><td>File was opened with read-only access.</td></tr><tr><td>#H5F_ACC_SWMR_WRITE</td><td>File was opened with read/write access for a single-writer/multiple-reader (SWMR) scenario. Note that the writer process must also open the file with the #H5F_ACC_RDWR flag.</td></tr><tr><td>#H5F_ACC_SWMR_READ</td><td>File was opened with read-only access for a single-writer/multiple-reader (SWMR) scenario. Note that the reader process must also open the file with the #H5F_ACC_RDONLY flag.</td></tr></table>"
@@ -186,5 +260,5 @@ ALIASES += scopes="<table><tr><td>#H5F_SCOPE_GLOBAL</td><td>Flushes the entire v
 ALIASES += sign_prop="<table><tr><td>#H5T_SGN_NONE</td><td>0</td><td>Unsigned integer type</td></tr><tr><td>#H5T_SGN_2</td><td>1</td><td>Two's complement signed integer type</td></tr></table>"
 ALIASES += storage_type="<table><tr><td>#H5G_STORAGE_TYPE_COMPACT</td><td>Compact storage</td></tr><tr><td>#H5G_STORAGE_TYPE_DENSE</td><td>Indexed storage</td></tr><tr><td>#H5G_STORAGE_TYPE_SYMBOL_TABLE</td><td>Symbol tables, the original HDF5 structure</td></tr></table>"
 ALIASES += str_pad_type="<table><tr><td>#H5T_STR_NULLTERM</td><td>0</td><td>Null terminate (as C does)</td></tr><tr><td>#H5T_STR_NULLPAD</td><td>1</td><td>Pad with zeros</td></tr><tr><td>#H5T_STR_SPACEPAD</td><td>2</td><td>Pad with spaces (as FORTRAN does)</td></tr></table>"
-ALIASES += virtual=" \see Supporting Functions: \li H5Pget_layout() \li H5Pset_layout() \li H5Sget_regular_hyperslab() \li H5Sis_regular_hyperslab() \li H5Sselect_hyperslab() \see VDS Functions: \li H5Pget_virtual_count() \li H5Pget_virtual_dsetname() \li H5Pget_virtual_filename() \li H5Pget_virtual_prefix() \li H5Pget_virtual_printf_gap() \li H5Pget_virtual_srcspace() \li H5Pget_virtual_view() \li H5Pget_virtual_vspace() \li H5Pset_virtual \li H5Pset_virtual_prefix() \li H5Pset_virtual_printf_gap() \li H5Pset_virtual_view()"
+ALIASES += see_virtual=" \see Supporting Functions: H5Pget_layout(), H5Pset_layout(), H5Sget_regular_hyperslab(), H5Sis_regular_hyperslab(), H5Sselect_hyperslab() \see VDS Functions: H5Pget_virtual_count(), H5Pget_virtual_dsetname(), H5Pget_virtual_filename(), H5Pget_virtual_prefix(), H5Pget_virtual_printf_gap(), H5Pget_virtual_srcspace(), H5Pget_virtual_view(), H5Pget_virtual_vspace(), H5Pset_virtual(), H5Pset_virtual_prefix(), H5Pset_virtual_printf_gap(), H5Pset_virtual_view()"
 ALIASES += obj_info_fields="<table><tr><th>Flag</th><th>Purpose</th></tr><tr><td>#H5O_INFO_BASIC</td><td>Fill in the fileno, addr, type, and rc fields</td></tr><tr> <td>#H5O_INFO_TIME</td><td>Fill in the atime, mtime, ctime, and btime fields</td></tr><tr> <td>#H5O_INFO_NUM_ATTRS</td> <td>Fill in the num_attrs field</td></tr><tr><td>#H5O_INFO_HDR</td><td>Fill in the num_attrs field</td></tr><tr><td>#H5O_INFO_META_SIZE</td><td>Fill in the meta_size field</td></tr><tr><td>#H5O_INFO_ALL</td><td>#H5O_INFO_BASIC | #H5O_INFO_TIME | #H5O_INFO_NUM_ATTRS | #H5O_INFO_HDR | #H5O_INFO_META_SIZE</td></tr></table>"