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-rw-r--r--MANIFEST3
-rwxr-xr-xconfigure24
-rw-r--r--configure.ac2
-rw-r--r--doxygen/CMakeLists.txt2
-rw-r--r--doxygen/aliases180
-rw-r--r--doxygen/dox/api-compat-macros.dox290
-rw-r--r--doxygen/img/IOFlow.gifbin0 -> 57285 bytes
-rw-r--r--doxygen/img/IOFlow2.gifbin0 -> 29805 bytes
-rw-r--r--doxygen/img/IOFlow3.gifbin0 -> 21442 bytes
-rw-r--r--src/H5Apublic.h13
-rw-r--r--src/H5Dpublic.h81
-rw-r--r--src/H5Epublic.h30
-rw-r--r--src/H5Fpublic.h30
-rw-r--r--src/H5Gpublic.h93
-rw-r--r--src/H5Ipublic.h42
-rw-r--r--src/H5Lpublic.h15
-rw-r--r--src/H5Opublic.h24
-rw-r--r--src/H5PLpublic.h11
-rw-r--r--src/H5Ppublic.h111
-rw-r--r--src/H5Rpublic.h13
-rw-r--r--src/H5Spublic.h14
-rw-r--r--src/H5Tpublic.h80
-rw-r--r--src/H5Zpublic.h67
-rw-r--r--src/H5public.h7
24 files changed, 802 insertions, 330 deletions
diff --git a/MANIFEST b/MANIFEST
index 8cfc8cd..570c1d7 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -253,6 +253,9 @@
./doxygen/img/FF-IH_FileObject.gif
./doxygen/img/FileFormatSpecChunkDiagram.jpg
./doxygen/img/HDFG-logo.png
+./doxygen/img/IOFlow.gif
+./doxygen/img/IOFlow2.gif
+./doxygen/img/IOFlow3.gif
./doxygen/img/PaletteExample1.gif
./doxygen/img/Palettes.fm.anc.gif
./doxygen/img/ftv2node.png
diff --git a/configure b/configure
index 9cb3406..f0c2c61 100755
--- a/configure
+++ b/configure
@@ -943,6 +943,7 @@ infodir
docdir
oldincludedir
includedir
+runstatedir
localstatedir
sharedstatedir
sysconfdir
@@ -1088,6 +1089,7 @@ datadir='${datarootdir}'
sysconfdir='${prefix}/etc'
sharedstatedir='${prefix}/com'
localstatedir='${prefix}/var'
+runstatedir='${localstatedir}/run'
includedir='${prefix}/include'
oldincludedir='/usr/include'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
@@ -1340,6 +1342,15 @@ do
| -silent | --silent | --silen | --sile | --sil)
silent=yes ;;
+ -runstatedir | --runstatedir | --runstatedi | --runstated \
+ | --runstate | --runstat | --runsta | --runst | --runs \
+ | --run | --ru | --r)
+ ac_prev=runstatedir ;;
+ -runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \
+ | --runstate=* | --runstat=* | --runsta=* | --runst=* | --runs=* \
+ | --run=* | --ru=* | --r=*)
+ runstatedir=$ac_optarg ;;
+
-sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
ac_prev=sbindir ;;
-sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
@@ -1477,7 +1488,7 @@ fi
for ac_var in exec_prefix prefix bindir sbindir libexecdir datarootdir \
datadir sysconfdir sharedstatedir localstatedir includedir \
oldincludedir docdir infodir htmldir dvidir pdfdir psdir \
- libdir localedir mandir
+ libdir localedir mandir runstatedir
do
eval ac_val=\$$ac_var
# Remove trailing slashes.
@@ -1630,6 +1641,7 @@ Fine tuning of the installation directories:
--sysconfdir=DIR read-only single-machine data [PREFIX/etc]
--sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com]
--localstatedir=DIR modifiable single-machine data [PREFIX/var]
+ --runstatedir=DIR modifiable per-process data [LOCALSTATEDIR/run]
--libdir=DIR object code libraries [EPREFIX/lib]
--includedir=DIR C header files [PREFIX/include]
--oldincludedir=DIR C header files for non-gcc [/usr/include]
@@ -8146,7 +8158,7 @@ $as_echo "yes" >&6; }
DOXYGEN_HTML_HEADER='$(SRCDIR)/doxygen/hdf5_header.html'
DOXYGEN_HTML_FOOTER='$(SRCDIR)/doxygen/hdf5_footer.html'
DOXYGEN_HTML_EXTRA_STYLESHEET='$(SRCDIR)/doxygen/hdf5doxy.css'
- DOXYGEN_HTML_EXTRA_FILES='$(SRCDIR)/doxygen/hdf5_navtree_hacks.js $(SRCDIR)/doxygen/img/ftv2node.png $(SRCDIR)/doxygen/img/ftv2pnode.png'
+ DOXYGEN_HTML_EXTRA_FILES='$(SRCDIR)/doxygen/hdf5_navtree_hacks.js $(SRCDIR)/doxygen/img/FF-IH_FileGroup.gif $(SRCDIR)/doxygen/img/FF-IH_FileObject.gif $(SRCDIR)/doxygen/img/FileFormatSpecChunkDiagram.jpg $(SRCDIR)/doxygen/img/ftv2node.png $(SRCDIR)/doxygen/img/ftv2pnode.png $(SRCDIR)/doxygen/img/HDFG-logo.png $(SRCDIR)/doxygen/img/IOFlow2.gif $(SRCDIR)/doxygen/img/IOFlow3.gif $(SRCDIR)/doxygen/img/IOFlow.gif $(SRCDIR)/doxygen/img/PaletteExample1.gif $(SRCDIR)/doxygen/img/Palettes.fm.anc.gif'
DOXYGEN_TAG_FILE=hdf5.tag
DOXYGEN_SERVER_BASED_SEARCH=NO
DOXYGEN_EXTERNAL_SEARCH=NO
@@ -25302,7 +25314,7 @@ else
We can't simply define LARGE_OFF_T to be 9223372036854775807,
since some C++ compilers masquerading as C compilers
incorrectly reject 9223372036854775807. */
-#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31))
int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
&& LARGE_OFF_T % 2147483647 == 1)
? 1 : -1];
@@ -25334,7 +25346,7 @@ rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
We can't simply define LARGE_OFF_T to be 9223372036854775807,
since some C++ compilers masquerading as C compilers
incorrectly reject 9223372036854775807. */
-#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31))
int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
&& LARGE_OFF_T % 2147483647 == 1)
? 1 : -1];
@@ -25390,7 +25402,7 @@ else
We can't simply define LARGE_OFF_T to be 9223372036854775807,
since some C++ compilers masquerading as C compilers
incorrectly reject 9223372036854775807. */
-#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31))
int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
&& LARGE_OFF_T % 2147483647 == 1)
? 1 : -1];
@@ -25422,7 +25434,7 @@ rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
We can't simply define LARGE_OFF_T to be 9223372036854775807,
since some C++ compilers masquerading as C compilers
incorrectly reject 9223372036854775807. */
-#define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
+#define LARGE_OFF_T ((((off_t) 1 << 31) << 31) - 1 + (((off_t) 1 << 31) << 31))
int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
&& LARGE_OFF_T % 2147483647 == 1)
? 1 : -1];
diff --git a/configure.ac b/configure.ac
index 2c472ca..e971a37 100644
--- a/configure.ac
+++ b/configure.ac
@@ -946,7 +946,7 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
DOXYGEN_HTML_HEADER='$(SRCDIR)/doxygen/hdf5_header.html'
DOXYGEN_HTML_FOOTER='$(SRCDIR)/doxygen/hdf5_footer.html'
DOXYGEN_HTML_EXTRA_STYLESHEET='$(SRCDIR)/doxygen/hdf5doxy.css'
- DOXYGEN_HTML_EXTRA_FILES='$(SRCDIR)/doxygen/hdf5_navtree_hacks.js $(SRCDIR)/doxygen/img/ftv2node.png $(SRCDIR)/doxygen/img/ftv2pnode.png'
+ DOXYGEN_HTML_EXTRA_FILES='$(SRCDIR)/doxygen/hdf5_navtree_hacks.js $(SRCDIR)/doxygen/img/FF-IH_FileGroup.gif $(SRCDIR)/doxygen/img/FF-IH_FileObject.gif $(SRCDIR)/doxygen/img/FileFormatSpecChunkDiagram.jpg $(SRCDIR)/doxygen/img/ftv2node.png $(SRCDIR)/doxygen/img/ftv2pnode.png $(SRCDIR)/doxygen/img/HDFG-logo.png $(SRCDIR)/doxygen/img/IOFlow2.gif $(SRCDIR)/doxygen/img/IOFlow3.gif $(SRCDIR)/doxygen/img/IOFlow.gif $(SRCDIR)/doxygen/img/PaletteExample1.gif $(SRCDIR)/doxygen/img/Palettes.fm.anc.gif'
DOXYGEN_TAG_FILE=hdf5.tag
DOXYGEN_SERVER_BASED_SEARCH=NO
DOXYGEN_EXTERNAL_SEARCH=NO
diff --git a/doxygen/CMakeLists.txt b/doxygen/CMakeLists.txt
index 36ce590..ca36ef1 100644
--- a/doxygen/CMakeLists.txt
+++ b/doxygen/CMakeLists.txt
@@ -21,7 +21,7 @@ if (DOXYGEN_FOUND)
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 ${HDF5_DOXYGEN_DIR}/img/ftv2pnode.png")
+ set (DOXYGEN_HTML_EXTRA_FILES "${HDF5_DOXYGEN_DIR}/hdf5_navtree_hacks.js ${HDF5_DOXYGEN_DIR}/img/FF-IH_FileGroup.gif ${HDF5_DOXYGEN_DIR}/img/FF-IH_FileObject.gif ${HDF5_DOXYGEN_DIR}/img/FileFormatSpecChunkDiagram.jpg ${HDF5_DOXYGEN_DIR}/img/ftv2node.png ${HDF5_DOXYGEN_DIR}/img/ftv2pnode.png ${HDF5_DOXYGEN_DIR}/img/HDFG-logo.png ${HDF5_DOXYGEN_DIR}/img/IOFlow2.gif ${HDF5_DOXYGEN_DIR}/img/IOFlow3.gif ${HDF5_DOXYGEN_DIR}/img/IOFlow.gif ${HDF5_DOXYGEN_DIR}/img/PaletteExample1.gif ${HDF5_DOXYGEN_DIR}/img/Palettes.fm.anc.gif")
set (DOXYGEN_TAG_FILE ${HDF5_BINARY_DIR}/hdf5.tag)
set (DOXYGEN_SERVER_BASED_SEARCH NO)
set (DOXYGEN_EXTERNAL_SEARCH NO)
diff --git a/doxygen/aliases b/doxygen/aliases
index 9b162c3..2ca29ef 100644
--- a/doxygen/aliases
+++ b/doxygen/aliases
@@ -22,6 +22,12 @@ ALIASES += hid_ti{1}="Returns an \1 identifier if successful; otherwise returns
ALIASES += hid_tv{1}="Returns an \1 identifier if successful; otherwise returns a negative value. "
ALIASES += htri_t="Returns zero (false), a positive (true) or a negative (failure) value."
+ALIASES += api_vers_2{3}="\1() is a macro that is mapped to either \2() or \3().\n\see \ref api-compat-macros"
+ALIASES += api_vers_3{4}="\1() is a macro that is mapped to either \2() or \3() or \4().\n\see \ref api-compat-macros"
+ALIASES += api_vers_4{5}="\1() is a macro that is mapped to either \2() or \3() or \4() or \5().\n\see \ref api-compat-macros"
+
+ALIASES += deprecation_note{1}="\deprecated Superseded by \1."
+
################################################################################
# General
################################################################################
@@ -42,6 +48,12 @@ 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
################################################################################
@@ -116,6 +128,13 @@ 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
################################################################################
@@ -136,6 +155,9 @@ 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"
@@ -148,8 +170,17 @@ 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 += vipl_id="\param[in] vipl_id VOL initialization property list identifier"
-ALIASES += vipl_id{1}="\param[in] \1 vipl_id VOL initialization 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"
@@ -157,6 +188,18 @@ 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"
+
+ALIASES += tcpl_id="\param[in] tcpl_id Datatype creation property list identifier"
+ALIASES += tcpl_id{1}="\param[in] \1 Datatype creation property list identifier"
+
+ALIASES += vipl_id="\param[in] vipl_id VOL initialization property list identifier"
+ALIASES += vipl_id{1}="\param[in] \1 vipl_id VOL initialization property list identifier"
+
################################################################################
# Objects
################################################################################
@@ -170,23 +213,149 @@ 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 += par_compr_note="\attention If you are planning to use compression with parallel HDF5, ensure that calls to H5Dwrite() occur in collective mode. In other words, all MPI ranks (in the relevant communicator) call H5Dwrite() and pass a dataset transfer property list with the MPI-IO collective option property set to #H5FD_MPIO_COLLECTIVE_IO.\n Note that data transformations are currently \Bold{not} supported when writing to datasets in parallel and with compression enabled."
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"
+
+################################################################################
+# RFCs
+################################################################################
+
+ALIASES += ref_rfc20210528="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_multi_thread.pdf\">Multi-Thread HDF5</a>"
+ALIASES += ref_rfc20210219="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/selection_io_RFC_210610.pdf\">Selection I/O</a>"
+ALIASES += ref_rfc20200213="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_VFD_subfiling_200424.pdf\">VFD Sub-filing</a>"
+ALIASES += ref_rfc20200210="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/Onion_VFD_RFC_211122.pdf\">Onion VFD</a>"
+ALIASES += ref_rfc20190923="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/2019-09-23-RFC_VOL_feature_flags.pdf\">Virtual Object Layer (VOL) API Compatibility</a>"
+ALIASES += ref_rfc20190715="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/var_len_data_sketch_design_190715.pdf\">Variable-Length Data in HDF5 Sketch Design</a>"
+ALIASES += ref_rfc20190410="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_VFD_Plugin.docx.pdf\">A Plugin Interface for HDF5 Virtual File Drivers</a>"
+ALIASES += ref_rfc20181231="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_Min_Obj_Headers_181231.pdf\">Dataset Object Header Size</a>"
+ALIASES += ref_rfc20181220="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/3.2.1_3.2.2_deliverable_181220_v4.pdf\">MS 3.2 – Addressing Scalability: Scalability of open, close, flush CASE STUDY: CGNS Hotspot analysis of CGNS cgp_open</a>"
+ALIASES += ref_rfc20180830="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_Sparse_Chunks180830.pdf\">Sparse Chunks</a>"
+ALIASES += ref_rfc20180829="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/mirror_VFD_RFC_2018-10-05.pdf\">H5FD_MIRROR Virtual File Driver</a>"
+ALIASES += ref_rfc20180815="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/splitter_VFD_RFC_180830.pdf\">Splitter_VFD</a>"
+ALIASES += ref_rfc20180620="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC-Chunking%20Functions-2018-06-20-v3.docx.pdf\">Chunk query functionality in HDF5</a>"
+ALIASES += ref_rfc20180610="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/VFD_SWMR_RFC_200916.pdf\">VFD SWMR</a>"
+ALIASES += ref_rfc20180321="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC-API_Contexts-2018-03-21.docx.pdf\">API Contexts</a>"
+ALIASES += ref_rfc20180125="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/enhance_h5clear.docx.pdf\">Enhancement to the tool <tt>h5clear</tt></a>"
+ALIASES += ref_rfc20170707="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/H5Sencode_format.docx.pdf\"><tt>H5Sencode/H5Sdecode</tt> Format Change</a>"
+ALIASES += ref_rfc20160105="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC-bounds.pdf\">Setting Bounds for Object Creation in HDF5 1.10.0</a>"
+ALIASES += ref_rfc20150915="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/2015-09-28-RFC-HDF5-1.10.0-File-Format-Superblock-Changes-EP.docx.pdf\">File Format Changes in HDF5 1.10.0</a>"
+ALIASES += ref_rfc20150709="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC-Page_Buffering.pdf\">Page Buffering</a>"
+ALIASES += ref_rfc20150615="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/cache_image_RFC_150929-QAK.docx.pdf\">Metadata Cache Image</a>"
+ALIASES += ref_rfc20150429="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/new_datatypes.pdf\">New Datatypes</a>"
+ALIASES += ref_rfc20150424="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC-CollectiveMetadataWrites.pdf\">Collective Metadata Writes</a>"
+ALIASES += ref_rfc20150423="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC-CollectiveMetadataReads.pdf\">Enabling Collective Metadata Reads</a>"
+ALIASES += ref_rfc20150301="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/sent_RFC_format_convert-v3.docx.pdf\">The Tool to Handle HDF5 File Format Compatibility for Chunked Datasets</a>"
+ALIASES += ref_rfc20150212="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_H5LTget_hardlinkds.docx.pdf\"><tt>H5LTget_hardlinks</tt> – High-level API to list all the hard links to an object</a>"
+ALIASES += ref_rfc20150205="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_F2003_v6.docx.pdf\">HDF5 Fortran Wrappers Maintenance: Dropping Support for Non-Fortran 2003 Standard Compliant Compilers</a>"
+ALIASES += ref_rfc20150202="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC%20New%20Autotools%20Behavior.docx.pdf\">New Autotools Behavior</a>"
+ALIASES += ref_rfc20141210="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/HDF5-VDS-requirements-use-cases-2014-12-10.pdf\">HDF5 Virtual Dataset</a>"
+ALIASES += ref_rfc20141201="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC%20filter%20memory%20issues%20on%20Windows.docx.pdf\">Allocate/Free Mismatches in HDF5 Filter Code on Windows</a>"
+ALIASES += ref_rfc20140916="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_VOL.pdf\">Virtual Object Layer</a>"
+ALIASES += ref_rfc20140827="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/CompressNChunk_RFC.pdf\">Chunking and Compression Performance Tool Requirements</a>"
+ALIASES += ref_rfc20140729="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/h5fis_accessible.pdf\">Replacing H5Fis_hdf5() with H5Fis_accessible()</a>"
+ALIASES += ref_rfc20140722="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/64bit_hid_t-v1.docx.pdf\">Switching to a 64-bit <tt>hid_t</tt> Space in HDF5</a>"
+ALIASES += ref_rfc20140717="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/analysis_ext.pdf\">Data Analysis Extensions</a>"
+ALIASES += ref_rfc20140707="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/2014-08-28-RFC_VOL.pdf\">Virtual Object Layer</a>"
+ALIASES += ref_rfc20140524="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC-Why%20does%20not%20compression%20work-GH-EP.docx.pdf\">HDF5 Compression Demystified</a>"
+ALIASES += ref_rfc20140318="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC%20H5free_memory%20v2.pdf\">Freeing Memory Allocated by the HDF5 Library</a>"
+ALIASES += ref_rfc20140313="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC-Compat-Tool-v2.docx.pdf\">Options to handle compatibility issues for HDF5 files</a>"
+ALIASES += ref_rfc20140224="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/Design-MetadataCache-Logging-THG20140224-v4.pdf\">Design: Metadata Cache Logging</a>"
+ALIASES += ref_rfc20131211="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC%20H5Ocork%20v5%20new%20fxn%20names.pdf\">Fine-Grained Control of Metadata Cache Flushes</a>"
+ALIASES += ref_rfc20130930="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC-Read-Attempts-for-Metadata-with-Checksum-v3.pdf\">Read Attempts for Metadata with Checksum</a>"
+ALIASES += ref_rfc20130919="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/core%20CFD%20paging%20v5.docx.pdf\">Core VFD Backing Store Paged Writes</a>"
+ALIASES += ref_rfc20130630="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/Design-HDF5-FlushDependencyTesting-20130630-v1.1.pdf\">Flush Dependency Testing</a>"
+ALIASES += ref_rfc20130316="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/HDF5DynamicallyLoadedFilters.pdf\">HDF5 Dynamically Loaded Filters</a>"
+ALIASES += ref_rfc20121114="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/DECTRIS%20Integration%20RFC%202012-11-29.pdf\">Direct Chunk Write</a>"
+ALIASES += ref_rfc20121024="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/FileSpaceManagement.pdf\">HDF5 File Space Management</a>"
+ALIASES += ref_rfc20120828="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/H5HPC_MultiDset_RW_IO_RFC_v4_20130320.docx.pdf\">New HDF5 API Routines for HPC Applications</a>"
+ALIASES += ref_rfc20120523="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/paged_aggregation.pdf\">HDF5 File Space Management: Paged Aggregation</a>"
+ALIASES += ref_rfc20120501="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/HDF5FileImageOperations.pdf\">HDF5 File Image Operations</a>"
+ALIASES += ref_rfc20120305="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC%20PHDF5%20Consistency%20Semantics%20MC%20120328.docx.pdf\">Enabling a Strict Consistency Semantics Model in Parallel HDF5</a>"
+ALIASES += ref_rfc20120220="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/h5repack_improve_hyperslab_over_chunked_dataset_v1.pdf\"><tt>h5repack</tt>: Improved Hyperslab selections for Large Chunked Datasets</a>"
+ALIASES += ref_rfc20120120="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/2012-1-25-Maintainers-guide-for-datatype.docx.pdf\">A Maintainer’s Guide for the Datatype Module in HDF5 Library</a>"
+ALIASES += ref_rfc20120104="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_actual_io_v4-1_done.docx.pdf\">Actual I/O Mode</a>"
+ALIASES += ref_rfc20111119="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC-H5Ocompare-review_v6.pdf\">New public functions to handle comparison</a>"
+ALIASES += ref_rfc20110825="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/2011-08-31-RFC_H5Ocopy_Named_DT_v2.docx.pdf\">Merging Named Datatypes in H5Ocopy()</a>"
+ALIASES += ref_rfc20110811="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_Enhancement_Hyperslab_Selection-1.4.docx.pdf\">Expanding the HDF5 Hyperslab Selection Interface</a>"
+ALIASES += ref_rfc20110726="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/metadata_aggregation_RFC_v03.docx.pdf\">HDF5 File Space Allocation and Aggregation</a>"
+ALIASES += ref_rfc20110614="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_h5dump_refactor_v3.docx.pdf\"> Refactor <tt>h5dump</tt> to Improve Maintenance</a>"
+ALIASES += ref_rfc20110329="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_Tools_Extlink_Cache_v3_r2.docx.pdf\">Support External Link Open File Cache in HDF5 Tools</a>"
+ALIASES += ref_rfc20110118="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC%20for%20h5diff%20Attribute%20Comparisons_v7.docx.pdf\"><tt>h5diff</tt> Attribute Comparisons</a>"
+ALIASES += ref_rfc20101122="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_swmr_timeouts_v2.docx.pdf\">SWMR Timeouts</a>"
+ALIASES += ref_rfc20101104="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/CacheExternalLinkFileOpens.pdf\">Caching Files Opened Through External Links</a>"
+ALIASES += ref_rfc20101018="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/HDF5-comparisons_v3-RFC-2011-08-03.pdf\">HDF5 File and Object Comparison Specification</a>"
+ALIASES += ref_rfc20100902="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/H5edit-RFC-Draft-v5.pdf\"><tt>h5edit</tt> – An HDF5 File Editing Tool</a>"
+ALIASES += ref_rfc20100727="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_HDF5_reservedCharacters-v2.pdf\">Reserved Characters for HDF5 Applications</a>"
+ALIASES += ref_rfc20100726="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/H5HPC_RFC-2010-09-28.pdf\">High-Level HDF5 API routines for HPC Applications</a>"
+ALIASES += ref_rfc20100511="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_h5diff_exclude_obj_v1_3.pdf\"><tt>h5diff</tt> – Exclude Object(s) from Comparison</a>"
+ALIASES += ref_rfc20100422="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_gen_attribute_tool_v2_f.pdf\">Generating attributes into an object with a tool</a>"
+ALIASES += ref_rfc20100312="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_Support_HDF518_in_Tools.pdf\">Supporting HDF5 1.8 in HDF5 Command Line Tools</a>"
+ALIASES += ref_rfc20091218="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RCF_h5diff_link_v1.2.docx.pdf\">Supporting soft-link and external-link for <tt>h5diff</tt></a>"
+ALIASES += ref_rfc20090907="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_Tools_Lib_v2.pdf\">HDF5 Tools Library Functions</a>"
+ALIASES += ref_rfc20090612="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_h5diff_default_epsilon.pdf\">Default EPSILON values for comparing floating point data</a>"
+ALIASES += ref_rfc20081218="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_h5diff_NonComparable.pdf\">Reporting of Non-Comparable Datasets by <tt>h5diff</tt></a>"
+ALIASES += ref_rfc20081205="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_elink_callback.pdf\">External Link Traversal Callback</a>"
+ALIASES += ref_rfc20081030="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_chunk_cache_functions.pdf\">Setting Raw Data Chunk Cache Parameters in HDF5</a>"
+ALIASES += ref_rfc20080915="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/FileFreeSpacePerformance.pdf\">Performance Report for Free-space Manager</a>"
+ALIASES += ref_rfc20080904="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/ExternalLinkFileAccessProperty.pdf\">Setting File Access Property List for accessing External Link</a>"
+ALIASES += ref_rfc20080728="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_Native_Time_Types.pdf\">Native Time Types in HDF5</a>"
+ALIASES += ref_rfc20080723="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_Special_Values_in_HDF5.pdf\">Special Values in HDF5</a>"
+ALIASES += ref_rfc20080301="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/DynamicTransformations_RFC.pdf\">Dynamic Transformations to HDF5 Data</a>"
+ALIASES += ref_rfc20080209="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC-Using-SVN-branching-Feb9.pdf\">Using SVN branching to improve software development process at THG</a>"
+ALIASES += ref_rfc20080206="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC-HIS-REL-1.8_Feb6.pdf\">Maintaining the <tt>HISTORY.txt</tt> and <tt>RELEASE.txt</tt> files in HDF5</a>"
+ALIASES += ref_rfc20071111="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/AURA-corruption-2007-11-12.pdf\">Addressing HDF5 file corruption issue</a>"
+ALIASES += ref_rfc20071018="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC_NaNsHDF5.pdf\"><tt>NaN</tt> detection in HDF5</a>"
+ALIASES += ref_rfc20070801="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/Metadata_Journaling_RFC.pdf\">Metadata Journaling to Improve Crash Survivability</a>"
+ALIASES += ref_rfc20070413="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/API_Compatibility_RFC.txt.pdf\">API Compatibility Strategies for HDF5</a>"
+ALIASES += ref_rfc20070115="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/PrivateHeap.pdf\">A \"Private\" Heap for HDF5</a>"
+ALIASES += ref_rfc20060623="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/coll_ind_dd6.pdf\">Performance Comparison of Collective I/O and Independent I/O with Derived Datatypes</a>"
+ALIASES += ref_rfc20060604="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/h5stat_spec_v3_2006-06-04.pdf\"><tt>h5stat</tt> tool</a>"
+ALIASES += ref_rfc20060505="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/Simple%20Performance%20Test%20on%20Fletcher32%20Filter.pdf\">Simple Performance Test on Fletcher32 Filter</a>"
+ALIASES += ref_rfc20060410="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/h5chk_Requirements.pdf\">Requirement Specifications of an HDF5 File Format Validation Tool</a>"
+ALIASES += ref_rfc20060317="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/sec2driver-RFC.pdf\">Proposed changes to the <tt>sec2</tt> driver </a>"
+ALIASES += ref_rfc20060124="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/FITS%20to%20HDF5%20mapping.pdf\">Mapping FITS data to HDF5</a>"
+ALIASES += ref_rfc20040811="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/text-dtype.htm.pdf\">Conversion Between Text and Datatype</a>"
+
+################################################################################
# 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>"
+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></table>"
ALIASES += id_types="<table><tr><td>#H5I_FILE</td><td>File</td></tr><tr><td>#H5I_GROUP</td><td>Group</td></tr><tr><td>#H5I_DATATYPE</td><td>Datatype</td></tr><tr><td>#H5I_DATASPACE</td><td>Dataspace</td></tr><tr><td>#H5I_DATASET</td><td>Dataset</td></tr><tr><td>#H5I_ATTR</td><td>Attribute</td></tr></table>"
ALIASES += indexes="<table><tr><td>#H5_INDEX_NAME</td><td>Lexicographic order on name</td></tr><tr><td>#H5_INDEX_CRT_ORDER</td><td>Index on creation order</td></tr></table>"
ALIASES += link_types="<table><tr><td>#H5L_TYPE_HARD</td><td>Hard link</td></tr><tr><td>#H5L_TYPE_SOFT</td><td>Soft link</td></tr><tr><td>#H5L_TYPE_EXTERNAL</td><td>External link</td></tr><tr><td>#H5L_TYPE_ERROR</td><td>Error</td></tr></table>"
@@ -199,4 +368,5 @@ 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 += 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>"
diff --git a/doxygen/dox/api-compat-macros.dox b/doxygen/dox/api-compat-macros.dox
index 4a1578d..9e8a297 100644
--- a/doxygen/dox/api-compat-macros.dox
+++ b/doxygen/dox/api-compat-macros.dox
@@ -300,296 +300,6 @@
-DH5Lget_info_vers=1 application.c
\endcode
- \subsubsection fun-options-112 Function Mapping Options in Releases 1.12.x
- <table>
- <tr>
- <th style="text-align: left;">Macro <br/> (\Code{H5xxx})</th>
- <th>Default function used if no macro specified
- <ul><li>Function/struct mapping:\Code{H5xxx_vers=N}</li></ul>
- </th>
- <th>Function used if specifying 1.10
- <ul><li>Function/struct mapping: \Code{H5xxx_vers=1}</li></ul>
- </th>
- </tr>
- <tr>
- <td>H5Lget_info()</td>
- <td>H5Lget_info2()
- <ul>
- <li>Function mapping:\Code{H5Lget_info_vers=2}</li>
- <li>Struct mapping:\Code{H5L_info_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Lget_info1()
- <ul>
- <li>Function mapping \Code{H5Lget_info_vers=1}</li>
- <li>Struct mapping: \Code{H5L_info_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Lget_info_by_idx()</td>
- <td>H5Lget_info_by_idx2()
- <ul>
- <li>Function mapping: \Code{H5Lget_info_by_idx_vers=2}</li>
- <li>Struct mapping: \Code{H5L_info_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Lget_info_by_idx1()
- <ul>
- <li>Function mapping: \Code{H5Lget_info_by_idx_vers=1}</li>
- <li>Struct mapping: \Code{H5L_info_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Literate()</td>
- <td>H5Literate2()
- <ul>
- <li>Function mapping: \Code{H5Literate_vers=2}</li>
- <li>Struct mapping: \Code{H5L_iterate_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Literate1()
- <ul>
- <li>Function mapping: \Code{H5Literate_vers=1}</li>
- <li>Struct mapping: \Code{H5L_iterate_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Literate_by_name()</td>
- <td>H5Literate_by_name2()
- <ul>
- <li>Function mapping: \Code{H5Literate_by_name_vers=2}</li>
- <li>Struct mapping: \Code{H5L_iterate_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Literate_by_name1()
- <ul>
- <li>Function mapping: \Code{H5Literate_by_name_vers=1}</li>
- <li>Struct mapping: \Code{H5L_iterate_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Lvisit()</td>
- <td>H5Lvisit2()
- <ul>
- <li>Function mapping: \Code{H5Lvisit_vers=2}</li>
- <li>Struct mapping: \Code{H5L_iterate_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Lvisit1()
- <ul>
- <li>Function mapping: \Code{H5Lvisit_vers=1}</li>
- <li>Struct mapping: \Code{H5L_iterate_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Lvisit_by_name()</td>
- <td>H5Lvisit_by_name2()
- <ul>
- <li>Function mapping: \Code{H5Lvisit_by_name_vers=2}</li>
- <li>Struct mapping: \Code{H5L_iterate_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Lvisit_by_name1()
- <ul>
- <li>Function mapping: \Code{H5Lvisit_by_name_vers=1}</li>
- <li>Struct mapping: \Code{H5L_iterate_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Oget_info()</td>
- <td>H5Oget_info3()
- <ul>
- <li>Function mapping: \Code{H5Oget_info_vers=3}</li>
- <li>Struct mapping: \Code{H5O_info_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Oget_info1()
- <ul>
- <li>Function mapping: \Code{H5Oget_info_vers=1}</li>
- <li>Struct mapping: \Code{H5O_info_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Oget_info_by_idx()</td>
- <td>H5Oget_info_by_idx3()
- <ul><li>Function mapping: \Code{H5Oget_info_by_idx_vers=3}</li>
- <li>Struct mapping: \Code{H5O_info_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Oget_info_by_idx1()
- <ul>
- <li>Function mapping: \Code{H5Oget_info_by_idx_vers=1}</li>
- <li>Struct mapping: \Code{H5O_info_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Oget_info_by_name()</td>
- <td>H5Oget_info_by_name3()
- <ul>
- <li>Function mapping: \Code{H5O_get_info_by_name_vers=3}</li>
- <li>Struct mapping: \Code{H5O_info_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Oget_info_by_name1()
- <ul>
- <li>Function mapping: \Code{H5O_get_info_by_name_vers=1}</li>
- <li>Struct mapping: \Code{H5O_info_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Ovisit()</td>
- <td>H5Ovisit3()
- <ul>
- <li>Function mapping: \Code{H5Ovisit_vers=3}</li>
- <li>Struct mapping: \Code{H5O_iterate_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Ovisit1()
- <ul><li>Function mapping: \Code{H5Ovisit_vers=1}</li>
- <li>Struct mapping: \Code{H5O_iterate_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Ovisit_by_name()</td>
- <td>H5Ovisit_by_name3()
- <ul>
- <li>Function mapping: \Code{H5Ovisit_by_name_vers=3}</li>
- <li>Struct mapping: \Code{H5O_iterate_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Ovisit_by_name1()
- <ul>
- <li>Function mapping: \Code{H5Ovisit_by_name_vers=1}</li>
- <li>Struct mapping: \Code{H5O_iterate_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Pencode()</td>
- <td>H5Pencode2()
- <ul>
- <li>Function mapping: \Code{H5Pencode_vers=2}</li>
- </ul>
- </td>
- <td>H5Pencode1()
- <ul>
- <li>Function mapping: \Code{H5Pencode_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Sencode()</td>
- <td>H5Sencode2()
- <ul>
- <li>Function mapping: \Code{H5Sencode_vers=2}</li>
- </ul>
- </td>
- <td>H5Sencode1()
- <ul>
- <li>Function mapping: \Code{H5Sencode_vers=1}</li>
- </ul>
- </td>
- </tr>
- </table>
-
- \subsubsection fun-options-110 Function Mapping Options in Releases 1.10.x
- <table>
- <tr>
- <th>Macro</th>
- <th>Default function used <br/> <sub>(if no macro specified)</sub></th>
- <th>Introduced in</th>
- <th>\Code{h5cc} version flag and value</th>
- <th>Mapped to function or struct</th>
- </tr>
- <tr>
- <td rowspan="2">H5Rdereference()</td>
- <td rowspan="2">H5Rdereference2()</td>
- <td rowspan="2">HDF5-1.10.0</td>
- <td>\Code{-DH5Rdereference_vers=1}</td>
- <td>H5Rdereference1()</td>
- </tr>
- <tr>
- <td>\Code{-DH5Rdereference_vers=2}</td>
- <td>H5Rdereference2()</td>
- </tr>
- <tr>
- <td rowspan="2">H5Fget_info()</td>
- <td rowspan="2">H5Fget_info2()</td>
- <td rowspan="2">HDF5-1.10.0</td>
- <td>\Code{-DH5Fget_info_vers=1}</td>
- <td>H5Fget_info1() with struct \ref H5F_info1_t</td>
- </tr>
- <tr>
- <td>\Code{-DH5Fget_info_vers=2}</td>
- <td>H5Fget_info2() with struct \ref H5F_info2_t</td>
- </tr>
- <tr>
- <td rowspan="2">H5Oget_info()</td>
- <td rowspan="2">H5Oget_info1()</td>
- <td rowspan="2">HDF5-1.10.3</td>
- <td>\Code{-DH5Oget_info_vers=1}</td>
- <td>H5Oget_info1()</td>
- </tr>
- <tr>
- <td>\Code{-DH5Oget_info_vers=2}</td>
- <td>H5Oget_info2()</td>
- </tr>
- <tr>
- <td rowspan="2">H5Oget_info_by_idx()</td>
- <td rowspan="2">H5Oget_info_by_idx1()</td>
- <td rowspan="2">HDF5-1.10.3</td>
- <td>\Code{-DH5Oget_info_by_idx_vers=1}</td>
- <td>H5Oget_info_by_idx1()</td>
- </tr>
- <tr>
- <td>\Code{-DH5Oget_info_by_idx_vers=2}</td>
- <td>H5Oget_info_by_idx2()</td>
- </tr>
- <tr>
- <td rowspan="2">H5Oget_info_by_name()</td>
- <td rowspan="2">H5Oget_info_by_name1()</td>
- <td rowspan="2">HDF5-1.10.3</td>
- <td>\Code{-DH5Oget_info_by_name_vers=1}</td>
- <td>H5Oget_info_by_name1()</td>
- </tr>
- <tr>
- <td>\Code{-DH5Oget_info_by_name_vers=2}</td>
- <td>H5Oget_info_by_name2()</td>
- </tr>
- <tr>
- <td rowspan="2">H5Ovisit()</td>
- <td rowspan="2">H5Ovisit1()</td>
- <td rowspan="2">HDF5-1.10.3</td>
- <td>\Code{-DH5Ovisit_vers=1}</td>
- <td>H5Ovisit1()</td>
- </tr>
- <tr>
- <td>\Code{-DH5Ovisit_vers=2}</td>
- <td>H5Ovisit2()</td>
- </tr>
- <tr>
- <td rowspan="2">H5Ovisit_by_name()</td>
- <td rowspan="2">H5Ovisit_by_name1()</td>
- <td rowspan="2">HDF5-1.10.3</td>
- <td>\Code{-DH5Ovisit_by_name_vers=1}</td>
- <td>H5Ovisit_by_name1()</td>
- </tr>
- <tr>
- <td>\Code{-DH5Ovisit_by_name_vers=2}</td>
- <td>H5Ovisit_by_name2()</td>
- </tr>
- </table>
-
\subsubsection fun-options-18 Function Mapping Options in Releases 1.8.x
At release 1.8.0, the API compatibility macros, function mapping compile-time
version flags and values, and corresponding versioned functions listed in the
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diff --git a/src/H5Apublic.h b/src/H5Apublic.h
index 0198668..2bd2686 100644
--- a/src/H5Apublic.h
+++ b/src/H5Apublic.h
@@ -11,6 +11,19 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+/**\defgroup H5A H5A
+ *
+ * Use the functions in this module to manage HDF5 attributes.
+ *
+ * Like HDF5 datasets, HDF5 attributes are array variables which have an element
+ * datatype and a shape (dataspace). However, they perform a different function:
+ * Attributes decorate other HDF5 objects, and are typically used to
+ * represent application metadata. Unlike datasets, the HDF5 library does not
+ * support partial I/O operations for attributes and they cannot be compressed
+ * or extended.
+ *
+ */
+
/*
* This file contains public declarations for the H5A module.
*/
diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index 1cfff22..5170f67 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -11,6 +11,16 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+/**\defgroup H5D H5D
+ *
+ * Use the functions in this module to manage HDF5 datasets, including the
+ * transfer of data between memory and disk and the description of dataset
+ * properties. Datasets are used by other HDF5 APIs and referenced either by
+ * name or by a handle. Such handles can be obtained by either creating or
+ * opening the dataset.
+ *
+ */
+
/*
* This file contains public declarations for the H5D module.
*/
@@ -130,16 +140,81 @@ typedef enum H5D_fill_value_t {
extern "C" {
#endif
-/* Define the operator function pointer for H5Diterate() */
+//! <!-- [H5D_operator_t_snip] -->
+/**
+ * \brief Callback for H5Diterate()
+ *
+ * \param[in,out] elem Pointer to the memory buffer containing the current dataset
+ * element
+ * \param[in] type_id Datatype identifier of the elements stored in \p elem
+ * \param[in] ndim Number of dimensions for the \p point array
+ * \param[in] point Array containing the location of the element within
+ * the original dataspace
+ * \param[in,out] operator_data Pointer to any user-defined data associated with
+ * the operation
+ * \return \herr_t_iter
+ *
+ */
typedef herr_t (*H5D_operator_t)(void *elem, hid_t type_id, unsigned ndim, const hsize_t *point,
void *operator_data);
+//! <!-- [H5D_operator_t_snip] -->
-/* Define the operator function pointer for H5Dscatter() */
+//! <!-- [H5D_scatter_func_t_snip] -->
+/**
+ * \brief Callback for H5Dscatter()
+ *
+ * \param[out] src_buf Pointer to the buffer holding the next set of elements to
+ * scatter. On entry, the value of where \p src_buf points to
+ * is undefined. The callback function should set \p src_buf
+ * to point to the next set of elements.
+ * \param[out] src_buf_bytes_used Pointer to the number of valid bytes in \p src_buf.
+ * On entry, the value where \p src_buf_bytes_used points
+ * to is undefined. The callback function should set
+ * \p src_buf_bytes_used to the of valid bytes in \p src_buf.
+ * This number must be a multiple of the datatype size.
+ * \param[in,out] op_data User-defined pointer to data required by the callback
+ * function. A pass-through of the \p op_data pointer provided
+ * with the H5Dscatter() function call.
+ * \return herr_t
+ *
+ * \details The callback function should always return at least one
+ * element in \p src_buf, and must not return more elements
+ * than are remaining to be scattered. This function will be
+ * repeatedly called until all elements to be scattered have
+ * been returned. The callback function should return zero (0)
+ * to indicate success, and a negative value to indicate failure.
+ *
+ */
typedef herr_t (*H5D_scatter_func_t)(const void **src_buf /*out*/, size_t *src_buf_bytes_used /*out*/,
void *op_data);
+//! <!-- [H5D_scatter_func_t_snip] -->
-/* Define the operator function pointer for H5Dgather() */
+//! <!-- [H5D_gather_func_t_snip] -->
+/**
+ * \brief Callback for H5Dgather()
+ *
+ * \param[in] dst_buf Pointer to the destination buffer which has been filled
+ * with the next set of elements gathered. This will always
+ * be identical to the \p dst_buf passed to H5Dgather()
+ * \param[in] dst_buf_bytes_used Pointer to the number of valid bytes in
+ * \p dst_buf. This number must be a multiple of
+ * the datatype size.
+ * \param[in,out] op_data User-defined pointer to data required by the callback
+ * function; a pass-through of the \p op_data pointer
+ * provided with the H5Dgather() function call.
+ * \returns \herr_t
+ *
+ * \details The callback function should process, store, or otherwise make use
+ * of the data returned in dst_buf before it returns, because the
+ * buffer will be overwritten unless it is the last call to the
+ * callback. This function will be repeatedly called until all gathered
+ * elements have been passed to the callback in dst_buf. The callback
+ * function should return zero (0) to indicate success, and a negative
+ * value to indicate failure.
+ *
+ */
typedef herr_t (*H5D_gather_func_t)(const void *dst_buf, size_t dst_buf_bytes_used, void *op_data);
+//! <!-- [H5D_gather_func_t_snip] -->
/**
* --------------------------------------------------------------------------
diff --git a/src/H5Epublic.h b/src/H5Epublic.h
index 3fd6cce..f95261a 100644
--- a/src/H5Epublic.h
+++ b/src/H5Epublic.h
@@ -11,6 +11,36 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+/**\defgroup H5E H5E
+ *
+ * Use the functions in this module to manage HDF5 error stacks and error
+ * messages.
+ *
+ * \internal The \c FUNC_ENTER macro clears the error stack whenever an
+ * interface function is entered. When an error is detected, an entry
+ * is pushed onto the stack. As the functions unwind, additional
+ * entries are pushed onto the stack. The API function will return
+ * some indication that an error occurred and the application can
+ * print the error stack.
+ *
+ * \internal Certain API functions in the \ref H5E package, such as H5Eprint(),
+ * do not clear the error stack. Otherwise, any function which does
+ * not have an underscore immediately after the package name will
+ * clear the error stack. For instance, H5Fopen() clears the error
+ * stack while \Code{H5F_open} does not.
+ *
+ * \internal An error stack has a fixed maximum size. If this size is exceeded
+ * then the stack will be truncated and only the inner-most functions
+ * will have entries on the stack. This is expected to be a rare
+ * condition.
+ *
+ * \internal Each thread has its own error stack, but since multi-threading has
+ * not been added to the library yet, this package maintains a single
+ * error stack. The error stack is statically allocated to reduce the
+ * complexity of handling errors within the \ref H5E package.
+ *
+ */
+
/*
* This file contains public declarations for the H5E module.
*/
diff --git a/src/H5Fpublic.h b/src/H5Fpublic.h
index 806320b..c44e729 100644
--- a/src/H5Fpublic.h
+++ b/src/H5Fpublic.h
@@ -11,6 +11,28 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+/**\defgroup H5F H5F
+ *
+ * Use the functions in this module to manage HDF5 files.
+ *
+ * In the code snippets below, we show the skeletal life cycle of an HDF5 file,
+ * when creating a new file (left) or when opening an existing file (right).
+ * File creation is essentially controlled through \ref FCPL, and file access to
+ * new and existing files is controlled through \ref FAPL. The file \c name and
+ * creation or access \c mode control the interaction with the underlying
+ * storage such as file systems.
+ *
+ * In addition to general file management functions, there are three categories
+ * of functions that deal with advanced file management tasks and use cases:
+ * 1. The control of the HDF5 \ref MDC
+ * 2. The use of (MPI-) \ref PH5F HDF5
+ *
+ * \defgroup MDC Metadata Cache
+ * \ingroup H5F
+ * \defgroup PH5F Parallel
+ * \ingroup H5F
+ */
+
/*
* This file contains public declarations for the H5F module.
*/
@@ -266,12 +288,6 @@ H5_DLL hid_t H5Fcreate(const char *filename, unsigned flags, hid_t fcpl_id, hid_
* \param[in] flags File access flags. Allowable values are:
* - #H5F_ACC_RDWR: Allows read and write access to file
* - #H5F_ACC_RDONLY: Allows read-only access to file
- * - #H5F_ACC_RDWR \c | #H5F_ACC_SWMR_WRITE: Indicates that
- * the file is open for writing in a
- * single-writer/multi-writer (SWMR) scenario.
- * - #H5F_ACC_RDONLY \c | #H5F_ACC_SWMR_READ: Indicates
- * that the file is open for reading in a
- * single-writer/multi-reader (SWMR) scenario.
* - An additional flag, #H5F_ACC_DEBUG, prints debug
* information. This flag can be combined with one of the
* above values using the bit-wise OR operator (\c |), but
@@ -344,8 +360,6 @@ H5_DLL hid_t H5Fcreate(const char *filename, unsigned flags, hid_t fcpl_id, hid_
* open call must include the file close degree setting
* #H5F_CLOSE_WEAK or the open will fail.
*
- * \version 1.10.0 The #H5F_ACC_SWMR_WRITE and #H5F_ACC_SWMR_READ flags were added.
- *
* \see H5Fclose()
*
*/
diff --git a/src/H5Gpublic.h b/src/H5Gpublic.h
index 7f1faf8..b8b0421 100644
--- a/src/H5Gpublic.h
+++ b/src/H5Gpublic.h
@@ -11,6 +11,99 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+/** \defgroup H5G H5G
+ *
+ * Use the functions in this module to manage HDF5 groups.
+ *
+ * \details \Bold{Groups in HDF5:} A group associates names with objects and
+ * provides a mechanism for mapping a name to an object. Since all
+ * objects appear in at least one group (with the possible exception of
+ * the root object) and since objects can have names in more than one
+ * group, the set of all objects in an HDF5 file is a directed
+ * graph. The internal nodes (nodes with out-degree greater than zero)
+ * must be groups while the leaf nodes (nodes with out-degree zero) are
+ * either empty groups or objects of some other type. Exactly one
+ * object in every non-empty file is the root object. The root object
+ * always has a positive in-degree because it is pointed to by the file
+ * super block.
+ *
+ * \Bold{Locating objects in the HDF5 file hierarchy:} An object name
+ * consists of one or more components separated from one another by
+ * slashes. An absolute name begins with a slash and the object is
+ * located by looking for the first component in the root object, then
+ * looking for the second component in the first object, etc., until
+ * the entire name is traversed. A relative name does not begin with a
+ * slash and the traversal begins at the location specified by the
+ * create or access function.
+ *
+ * \Bold{Group implementations in HDF5:} The original HDF5 group
+ * implementation provided a single indexed structure for link
+ * storage. A new group implementation, in HDF5 Release 1.8.0, enables
+ * more efficient compact storage for very small groups, improved link
+ * indexing for large groups, and other advanced features.
+ *
+ * \li The \Emph{original indexed} format remains the default. Links
+ * are stored in a B-tree in the group’s local heap.
+ * \li Groups created in the new \Emph{compact-or-indexed} format, the
+ * implementation introduced with Release 1.8.0, can be tuned for
+ * performance, switching between the compact and indexed formats
+ * at thresholds set in the user application.
+ * - The \Emph{compact} format will conserve file space and processing
+ * overhead when working with small groups and is particularly
+ * valuable when a group contains no links. Links are stored
+ * as a list of messages in the group’s header.
+ * - The \Emph{indexed} format will yield improved
+ * performance when working with large groups, e.g., groups
+ * containing thousands to millions of members. Links are stored in
+ * a fractal heap and indexed with an improved B-tree.
+ * \li The new implementation also enables the use of link names consisting of
+ * non-ASCII character sets (see H5Pset_char_encoding()) and is
+ * required for all link types other than hard or soft links, e.g.,
+ * external and user-defined links (see the \ref H5L APIs).
+ *
+ * The original group structure and the newer structures are not
+ * directly interoperable. By default, a group will be created in the
+ * original indexed format. An existing group can be changed to a
+ * compact-or-indexed format if the need arises; there is no capability
+ * to change back. As stated above, once in the compact-or-indexed
+ * format, a group can switch between compact and indexed as needed.
+ *
+ * Groups will be initially created in the compact-or-indexed format
+ * only when one or more of the following conditions is met:
+ * \li The low version bound value of the library version bounds property
+ * has been set to Release 1.8.0 or later in the file access property
+ * list (see H5Pset_libver_bounds()). Currently, that would require an
+ * H5Pset_libver_bounds() call with the low parameter set to
+ * #H5F_LIBVER_LATEST.\n When this property is set for an HDF5 file,
+ * all objects in the file will be created using the latest available
+ * format; no effort will be made to create a file that can be read by
+ * older libraries.
+ * \li The creation order tracking property, #H5P_CRT_ORDER_TRACKED, has been
+ * set in the group creation property list (see H5Pset_link_creation_order()).
+ *
+ * An existing group, currently in the original indexed format, will be
+ * converted to the compact-or-indexed format upon the occurrence of
+ * any of the following events:
+ * \li An external or user-defined link is inserted into the group.
+ * \li A link named with a string composed of non-ASCII characters is
+ * inserted into the group.
+ *
+ * The compact-or-indexed format offers performance improvements that
+ * will be most notable at the extremes, i.e., in groups with zero
+ * members and in groups with tens of thousands of members. But
+ * measurable differences may sometimes appear at a threshold as low as
+ * eight group members. Since these performance thresholds and criteria
+ * differ from application to application, tunable settings are
+ * provided to govern the switch between the compact and indexed
+ * formats (see H5Pset_link_phase_change()). Optimal thresholds will
+ * depend on the application and the operating environment.
+ *
+ * Future versions of HDF5 will retain the ability to create, read,
+ * write, and manipulate all groups stored in either the original
+ * indexed format or the compact-or-indexed format.
+ *
+ */
+
/*-------------------------------------------------------------------------
*
* Created: H5Gpublic.h
diff --git a/src/H5Ipublic.h b/src/H5Ipublic.h
index 7e1ce75..2e66b36 100644
--- a/src/H5Ipublic.h
+++ b/src/H5Ipublic.h
@@ -11,6 +11,48 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+/**\defgroup H5I H5I
+ *
+ * Use the functions in this module to manage identifiers defined by the HDF5
+ * library. See \ref H5IUD for user-defined identifiers and identifier
+ * types.
+ *
+ * HDF5 identifiers are usually created as a side-effect of creating HDF5
+ * entities such as groups, datasets, attributes, or property lists.
+ *
+ * Identifiers defined by the HDF5 library can be used to retrieve information
+ * such as path names and reference counts, and their validity can be checked.
+ *
+ * Identifiers can be updated by manipulating their reference counts.
+ *
+ * Unused identifiers should be reclaimed by closing the associated item, e.g.,
+ * HDF5 object, or decrementing the reference count to 0.
+ *
+ * \note Identifiers (of type \ref hid_t) are run-time auxiliaries and
+ * not persisted in the file.
+ *
+ * \defgroup H5IUD User-defined ID Types
+ * \ingroup H5I
+ *
+ * The \ref H5I module contains functions to define new identifier types.
+ * For convenience, handles of type \ref hid_t can then be associated with the
+ * new identifier types and user objects.
+ *
+ * New identifier types can be created by registering a new identifier type
+ * with the HDF5 library. Once a new identifier type has bee registered,
+ * it can be used to generate identifiers for user objects.
+ *
+ * User-defined identifier types can be searched and iterated.
+ *
+ * Like library-defined identifiers, user-defined identifiers \Emph{and}
+ * identifier types are reference counted, and the reference counts can be
+ * manipulated accordingly.
+ *
+ * User-defined identifiers no longer in use should be deleted or reclaimed,
+ * and identifier types should be destroyed if they are no longer required.
+ *
+ */
+
/*
* This file contains function prototypes for each exported function in
* the H5I module.
diff --git a/src/H5Lpublic.h b/src/H5Lpublic.h
index d78efda..2896ba4 100644
--- a/src/H5Lpublic.h
+++ b/src/H5Lpublic.h
@@ -11,6 +11,16 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+/**\defgroup H5L H5L
+ *
+ * Use the functions in this module to manage HDF5 links and link types.
+ *
+ * \defgroup TRAV Link Traversal
+ * \ingroup H5L
+ * \defgroup H5LA Advanced Link Functions
+ * \ingroup H5L
+ */
+
/*-------------------------------------------------------------------------
*
* Created: H5Lpublic.h
@@ -1238,7 +1248,7 @@ H5_DLL herr_t H5Lcreate_ud(hid_t link_loc_id, const char *link_name, H5L_type_t
* Remaining \c struct members are optional and may be passed as NULL.
*
* The link class passed in \c class_id must be in the user-definable
- * range between #H5L_TYPE_UD_MIN and #H5L_TYPE_UD_MAX
+ * range between #H5L_TYPE_UD_MIN and #H5L_TYPE_MAX
* (see the table below) and will override
* any existing link class with that identifier.
*
@@ -1284,7 +1294,7 @@ H5_DLL herr_t H5Lcreate_ud(hid_t link_loc_id, const char *link_name, H5L_type_t
* <tr>
* <td>255</td>
* <td>Maximum user-defined value</td>
- * <td>#H5L_TYPE_UD_MAX</td>
+ * <td>#H5L_TYPE_MAX</td>
* </tr>
* <tr>
* <td>255</td>
@@ -1339,7 +1349,6 @@ H5_DLL herr_t H5Lcreate_ud(hid_t link_loc_id, const char *link_name, H5L_type_t
* \li #H5L_TYPE_MAX is the maximum allowed value for a link type
* identifier.
* \li #H5L_TYPE_UD_MIN equals #H5L_TYPE_EXTERNAL.
- * \li #H5L_TYPE_UD_MAX equals #H5L_TYPE_MAX.
* \li #H5L_TYPE_ERROR indicates that an error has occurred.
*
* \note \Bold{Registration with The HDF Group:}\n
diff --git a/src/H5Opublic.h b/src/H5Opublic.h
index 0931f9b..24bf397 100644
--- a/src/H5Opublic.h
+++ b/src/H5Opublic.h
@@ -11,6 +11,30 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+/**\defgroup H5O H5O
+ *
+ * Use the functions in this module to manage HDF5 objects.
+ *
+ * HDF5 objects (groups, datasets, datatype objects) are usually created
+ * using functions in the object-specific modules (\ref H5G, \ref H5D,
+ * \ref H5T). However, new objects can also be created by copying existing
+ * objects.
+ *
+ * Many functions in this module are variations on object introspection,
+ * that is, the retrieval of detailed information about HDF5 objects in a file.
+ * Objects in an HDF5 file can be "visited" in an iterative fashion.
+ *
+ * HDF5 objects are usually updated using functions in the object-specific
+ * modules. However, there are certain generic object properties, such as
+ * reference counts, that can be manipulated using functions in this module.
+ *
+ * HDF5 objects are deleted as a side effect of rendering them unreachable
+ * from the root group. The net effect is the diminution of the object's
+ * reference count to zero, which can (but should not usually) be effected
+ * by a function in this module.
+ *
+ */
+
/*-------------------------------------------------------------------------
*
* Created: H5Opublic.h
diff --git a/src/H5PLpublic.h b/src/H5PLpublic.h
index 6bf46bf..7bcd817 100644
--- a/src/H5PLpublic.h
+++ b/src/H5PLpublic.h
@@ -10,6 +10,17 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+/**\defgroup H5PL H5PL
+ *
+ * Use the functions in this module to manage the loading behavior of HDF5
+ * plugins.
+ *
+ * \attention The loading behavior of HDF5 plugins can be controlled via the
+ * functions described below and certain environment variables, such
+ * as \c HDF5_PLUGIN_PRELOAD and \c HDF5_PLUGIN_PATH.
+ *
+ */
+
/*
* This file contains public declarations for the H5PL module.
*/
diff --git a/src/H5Ppublic.h b/src/H5Ppublic.h
index 2cac8b8..962552f 100644
--- a/src/H5Ppublic.h
+++ b/src/H5Ppublic.h
@@ -11,6 +11,103 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+/**\defgroup H5P H5P
+ *
+ * Use the functions in this module to manage HDF5 property lists and property
+ * list classes. HDF5 property lists are the main vehicle to configure the
+ * behavior of HDF5 API functions.
+ *
+ * Typically, property lists are created by instantiating one of the built-in
+ * or user-defined property list classes. After adding suitable properties,
+ * property lists are used when opening or creating HDF5 items, or when reading
+ * or writing data. Property lists can be modified by adding or changing
+ * properties. Property lists are deleted by closing the associated handles.
+ *
+ * \defgroup ALCAPL Attribute and Link Creation Properties
+ * \ingroup H5P
+ * Currently, there are only two creation properties that you can use to control
+ * the creation of HDF5 attributes and links. The first creation property, the
+ * choice of a character encoding, applies to both attributes and links.
+ * The second creation property applies to links only, and advises the library
+ * to automatically create missing intermediate groups when creating new objects.
+ *
+ * \defgroup DAPL Dataset Access Properties
+ * \ingroup H5P
+ * Use dataset access properties to modify the default behavior of the HDF5
+ * library when accessing datasets. The properties include adjusting the size
+ * of the chunk cache, providing prefixes for external content and virtual
+ * dataset file paths, and controlling flush behavior, etc. These properties
+ * are \Emph{not} persisted with datasets, and can be adjusted at runtime before
+ * a dataset is created or opened.
+ *
+ * \defgroup DCPL Dataset Creation Properties
+ * \ingroup H5P
+ * Use dataset creation properties to control aspects of dataset creation such
+ * as fill time, storage layout, compression methods, etc.
+ * Unlike dataset access and transfer properties, creation properties \Emph{are}
+ * stored with the dataset, and cannot be changed once a dataset has been
+ * created.
+ *
+ * \defgroup DXPL Dataset Transfer Properties
+ * \ingroup H5P
+ * Use dataset transfer properties to customize certain aspects of reading
+ * and writing datasets such as transformations, MPI-IO I/O mode, error
+ * detection, etc. These properties are \Emph{not} persisted with datasets,
+ * and can be adjusted at runtime before a dataset is read or written.
+ *
+ * \defgroup FAPL File Access Properties
+ * \ingroup H5P
+ * Use file access properties to modify the default behavior of the HDF5
+ * library when accessing files. The properties include selecting a virtual
+ * file driver (VFD), configuring the metadata cache (MDC), control
+ * file locking, etc. These properties are \Emph{not} persisted with files, and
+ * can be adjusted at runtime before a file is created or opened.
+ *
+ * \defgroup FCPL File Creation Properties
+ * \ingroup H5P
+ * Use file creation properties to control aspects of file creation such
+ * as setting a file space management strategy or creating a user block.
+ * Unlike file access properties, creation properties \Emph{are}
+ * stored with the file, and cannot be changed once a file has been
+ * created.
+ *
+ * \defgroup GAPL General Access Properties
+ * \ingroup H5P
+ * \todo Should this be as standalone page?
+ *
+ * \defgroup GCPL Group Creation Properties
+ * \ingroup H5P
+ * Use group creation properties to control aspects of group creation such
+ * as storage layout, compression, and link creation order tracking.
+ * Unlike file access properties, creation properties \Emph{are}
+ * stored with the group, and cannot be changed once a group has been
+ * created.
+ *
+ * \defgroup GPLO General Property List Operations
+ * \ingroup H5P
+ *
+ * Use the functions in this module to manage HDF5 property lists.
+ *
+ * \defgroup GPLOA General Property List Operations (Advanced)
+ * \ingroup H5P
+ *
+ * You can create and customize user-defined property list classes using the
+ * functions described below. Arbitrary user-defined properties can also
+ * be inserted into existing property lists as so-called temporary properties.
+ *
+ * \defgroup LAPL Link Access Properties
+ * \ingroup H5P
+ *
+ * \defgroup MAPL Map Access Properties
+ * \ingroup H5P
+ * \defgroup OCPL Object Creation Properties
+ * \ingroup H5P
+ *
+ * \defgroup OCPPL Object Copy Properties
+ * \ingroup H5P
+ *
+ */
+
/*
* This file contains function prototypes for each exported function in the
* H5P module.
@@ -3572,10 +3669,8 @@ H5_DLL herr_t H5Pget_small_data_block_size(hid_t fapl_id, hsize_t *size /*out*/)
* the file. For MPI IO and other parallel systems, choose an
* alignment which is a multiple of the disk block size.
*
- * If the file space handling strategy is set to
- * #H5F_FSPACE_STRATEGY_PAGE, then the alignment set via this
- * routine is ignored. The file space handling strategy is set
- * by H5Pset_file_space_strategy().
+ * The file space handling strategy is set by
+ * H5Pset_file_space_strategy().
*
* \since 1.0.0
*
@@ -4690,8 +4785,6 @@ H5_DLL herr_t H5Pget_fill_value(hid_t plist_id, hid_t type_id, void *value /*out
* - #H5D_CHUNKED: Raw data is stored separately from the object
* header in chunks in separate locations in the
* file.
- * - #H5D_VIRTUAL: Raw data is drawn from multiple datasets in
- * different files.
* \return
* Otherwise, returns a negative value indicating failure.
*
@@ -4703,8 +4796,6 @@ H5_DLL herr_t H5Pget_fill_value(hid_t plist_id, hid_t type_id, void *value /*out
* the dataset with parallel applications. See the H5Dwrite()
* documentation for details.
*
- * \version 1.10.0 #H5D_VIRTUAL added in this release.
- *
* \since 1.0.0
*
*/
@@ -5007,13 +5098,11 @@ H5_DLL herr_t H5Pset_shuffle(hid_t plist_id);
* - #H5D_CHUNKED: Store raw data separately from the object header
* as chunks of data in separate locations in
* the file.
- * - #H5D_VIRTUAL: Draw raw data from multiple datasets in
- * different files.
*
* Note that a compact storage layout may affect writing data to
* the dataset with parallel applications. See the note in
* H5Dwrite() documentation for details.
- * \version 1.10.0 #H5D_VIRTUAL added in this release.
+ *
* \since 1.0.0
*
*/
diff --git a/src/H5Rpublic.h b/src/H5Rpublic.h
index 81ae514..4ba7da1 100644
--- a/src/H5Rpublic.h
+++ b/src/H5Rpublic.h
@@ -11,6 +11,15 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+/**
+ * \defgroup H5R H5R
+ *
+ * Use the functions in this module to manage HDF5 references. Referents can
+ * be HDF5 objects, attributes, and selections on datasets a.k.a. dataset
+ * regions.
+ *
+ */
+
/*
* This file contains public declarations for the H5R module.
*/
@@ -127,7 +136,7 @@ H5_DLL herr_t H5Rcreate(void *ref, hid_t loc_id, const char *name, H5R_type_t re
*
* \brief Opens the HDF5 object referenced
*
- * \obj_id
+ * \dset_id{dataset}
* \param[in] ref_type The reference type of \p ref
* \param[in] ref Reference to open
*
@@ -199,7 +208,7 @@ H5_DLL hid_t H5Rget_region(hid_t dataset, H5R_type_t ref_type, const void *ref);
* \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[in] _ref Reference to query
* \param[out] obj_type Type of referenced object
*
* \return \herr_t
diff --git a/src/H5Spublic.h b/src/H5Spublic.h
index 7291c84..dbe0a51 100644
--- a/src/H5Spublic.h
+++ b/src/H5Spublic.h
@@ -11,6 +11,20 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+/**\defgroup H5S H5S
+ *
+ * Use the functions in this module to manage HDF5 dataspaces \Emph{and} selections.
+ *
+ * HDF5 dataspaces describe the \Emph{shape} of datasets in memory or in HDF5
+ * files. Dataspaces can be empty (#H5S_NULL), a singleton (#H5S_SCALAR), or
+ * a multi-dimensional, regular grid (#H5S_SIMPLE). Dataspaces can be re-shaped.
+ *
+ * Subsets of dataspaces can be "book-marked" or used to restrict I/O operations
+ * using \Emph{selections}. Furthermore, certain set operations are supported
+ * for selections.
+ *
+ */
+
/*
* This file contains public declarations for the H5S module.
*/
diff --git a/src/H5Tpublic.h b/src/H5Tpublic.h
index b34138b..b5dc566 100644
--- a/src/H5Tpublic.h
+++ b/src/H5Tpublic.h
@@ -11,6 +11,86 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+/**\defgroup H5T H5T
+ *
+ * Use the functions in this module to manage HDF5 datatypes.
+ *
+ * HDF5 datatypes describe the element type of HDF5 datasets and attributes.
+ * There's a large set of predefined datatypes, but users may find it useful
+ * to define new datatypes through a process called \Emph{derivation}.
+ *
+ * The element type is automatically persisted as part of the HDF5 metadata of
+ * attributes and datasets. Additionally, datatype definitions can be persisted
+ * to HDF5 files and linked to groups as HDF5 datatype objects or so-called
+ * \Emph{committed datatypes}.
+ *
+ * \defgroup ARRAY Array Datatypes
+ * \ingroup H5T
+ * \defgroup ATOM Atomic Datatypes
+ * \ingroup H5T
+ * \defgroup COMPOUND Compound Datatypes
+ * \ingroup H5T
+ * \defgroup CONV Conversion Function
+ * \ingroup H5T
+ * \defgroup ENUM Enumeration Datatypes
+ * \ingroup H5T
+ * \defgroup OPAQUE Opaque Datatypes
+ * \ingroup H5T
+ * \defgroup VLEN Variable-length Sequence Datatypes
+ * \ingroup H5T
+ *
+ * \defgroup PDT Predefined Datatypes
+ * \ingroup H5T
+ * \details What is a predefined HDF5 datatype?
+ * \todo Fill in the blanks!
+ *
+ * \defgroup PDTCPU By CPU
+ * \ingroup PDT
+ * \details CPU-specific datatypes
+ * \defgroup PDTALPHA DEC Alpha
+ * \ingroup PDTCPU
+ * \defgroup PDTX86 AMD & INTEL
+ * \ingroup PDTCPU
+ * \defgroup PDTMIPS SGI MIPS
+ * \ingroup PDTCPU
+ *
+ * \defgroup PDTIEEE IEEE
+ * \ingroup PDT
+ * \details The IEEE floating point types in big- and little-endian byte orders.
+ *
+ * \defgroup PDTSTD Standard Datatypes
+ * \ingroup PDT
+ * \details These are "standard" types. For instance, signed (2's complement)
+ * and unsigned integers of various sizes in big- and little-endian
+ * byte orders.
+ *
+ * \defgroup PDTUNIX UNIX-specific Datatypes
+ * \ingroup PDT
+ * \details Types which are particular to Unix.
+ * \todo Fill in the blanks!
+ *
+ * \defgroup PDTNAT Native Datatypes
+ * \ingroup PDT
+ * \details These are the datatypes detected during library \Emph{compilation}
+ * by \c H5detect(). Their names differ from other HDF5 datatype names
+ * as follows:
+ * \li Instead of a class name, precision and byte order as the last
+ * component, they have a C-like type name.
+ * \li If the type begins with \c U then it is the unsigned version of
+ * the integer type; other integer types are signed.
+ * \li The datatype \c LLONG corresponds C's \Code{long long} and
+ * \c LDOUBLE is \Code{long double}. These types might be the same
+ * as \c LONG and \c DOUBLE, respectively.
+ * \defgroup PDTC9x C9x Integer Datatypes
+ * \ingroup PDTNAT
+ * \details C9x integer types
+ * \todo Fill in the blanks!
+ *
+ * \defgroup PDTS Strings
+ * \ingroup PDT
+ *
+ */
+
/*
* This file contains public declarations for the H5T module.
*/
diff --git a/src/H5Zpublic.h b/src/H5Zpublic.h
index 90277cf..e1b3312 100644
--- a/src/H5Zpublic.h
+++ b/src/H5Zpublic.h
@@ -11,6 +11,73 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+/**\defgroup H5Z H5Z
+ *
+ * Use the functions in this module to manage HDF5 filters.
+ *
+ * User-defined filters are created by registering a filter descriptor of
+ * type #H5Z_class_t with the library.
+ *
+ * Available filters can be read or examined at runtime.
+ *
+ * It is conceivable that filters are stateful and that that state be
+ * updated at runtime.
+ *
+ * Filters are deleted by unregistering.
+ *
+ * HDF5 supports a filter pipeline that provides the capability for standard and
+ * customized raw data processing during I/O operations. HDF5 is distributed
+ * with a small set of standard filters such as compression (gzip, SZIP, and a
+ * shuffling algorithm) and error checking (Fletcher32 checksum). For further
+ * flexibility, the library allows a user application to extend the pipeline
+ * through the creation and registration of customized filters.
+ *
+ * The flexibility of the filter pipeline implementation enables the definition
+ * of additional filters by a user application. A filter
+ * \li is associated with a dataset when the dataset is created,
+ * \li can be used only with chunked data (i.e., datasets stored in the
+ * #H5D_CHUNKED storage layout), and
+ * \li is applied independently to each chunk of the dataset.
+ *
+ * The HDF5 library does not support filters for contiguous datasets because of
+ * the difficulty of implementing random access for partial I/O. Compact dataset
+ * filters are not supported because it would not produce significant results.
+ *
+ * Filter identifiers for the filters distributed with the HDF5
+ * Library are as follows:
+ * <table>
+ * <tr><td>#H5Z_FILTER_DEFLATE</td><td>The gzip compression, or
+ * deflation, filter</td></tr>
+ * <tr><td>#H5Z_FILTER_SZIP</td><td>The SZIP compression
+ * filter</td></tr>
+ * <tr><td>#H5Z_FILTER_NBIT</td><td>The N-bit compression
+ * filter</td></tr>
+ * <tr><td>#H5Z_FILTER_SCALEOFFSET</td><td>The scale-offset
+ * compression filter</td></tr>
+ * <tr><td>#H5Z_FILTER_SHUFFLE</td><td>The shuffle algorithm
+ * filter</td></tr>
+ * <tr><td>#H5Z_FILTER_FLETCHER32</td><td>The Fletcher32 checksum,
+ * or error checking, filter</td></tr>
+ * </table>
+ * Custom filters that have been registered with the library will have
+ * additional unique identifiers.
+ *
+ * See \ref_dld_filters for more information on how an HDF5 application can
+ * apply a filter that is not registered with the HDF5 library.
+ *
+ * \defgroup H5ZPRE Predefined Filters
+ * \ingroup H5Z
+ * \defgroup FLETCHER32 Checksum Filter
+ * \ingroup H5ZPRE
+ * \defgroup SCALEOFFSET Scale-Offset Filter
+ * \ingroup H5ZPRE
+ * \defgroup SHUFFLE Shuffle Filter
+ * \ingroup H5ZPRE
+ * \defgroup SZIP Szip Filter
+ * \ingroup H5ZPRE
+ *
+ */
+
/* Programmer: Robb Matzke
* Thursday, April 16, 1998
*/
diff --git a/src/H5public.h b/src/H5public.h
index 730e3de..3c90c2a 100644
--- a/src/H5public.h
+++ b/src/H5public.h
@@ -11,6 +11,13 @@
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+/**\defgroup H5 H5
+ *
+ * Use the functions in this module to manage the life cycle of HDF5 library
+ * instances.
+ *
+ */
+
/*
* This file contains public declarations for the HDF5 module.
*/
generated by cgit v0.12 at 2024-11-10 18:31:48 (GMT)