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Hdf5 1 10 doxygen merges #684

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May 26, 2021
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ebe023d
HDFFV-10865 - merge from dev, HDFArray perf fix.
byrnHDF Dec 29, 2020
cc749db
Remove duplicate setting
byrnHDF Jan 4, 2021
5e6ecc2
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Jan 11, 2021
a9227df
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Jan 23, 2021
12c9d1a
Whitespace changes after clang format
byrnHDF Jan 27, 2021
55d3565
Undo version 11 clang format changes
byrnHDF Jan 28, 2021
ee4ebd3
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Feb 1, 2021
51e5378
Merge CMake changes from develop
byrnHDF Feb 1, 2021
bbc9609
test testing script merge from develop
byrnHDF Feb 1, 2021
a8ae83d
Update supported platforms
byrnHDF Feb 2, 2021
02f185b
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Feb 4, 2021
39d6885
PR#3 merge from develop
byrnHDF Feb 4, 2021
28e5eb4
Merge gcc 10 diagnostics option from develop
byrnHDF Feb 8, 2021
678653c
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Feb 9, 2021
55368fa
Merge #318 OSX changes from develop
byrnHDF Feb 9, 2021
c74c09c
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Feb 9, 2021
d8011e2
Merge small changes from develop
byrnHDF Feb 16, 2021
516ac71
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Feb 17, 2021
a6de013
Minor non-space formatting changes
byrnHDF Feb 18, 2021
4b17412
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Feb 19, 2021
7faebce
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Feb 24, 2021
1e21839
#386 copyright corrections for java folder
byrnHDF Feb 26, 2021
a80a571
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Mar 1, 2021
4d7a150
Merges from develop
byrnHDF Mar 2, 2021
e8df4b9
Merge updates
byrnHDF Mar 3, 2021
86563f0
format fix
byrnHDF Mar 3, 2021
7fa5973
Fix missing underscore and make H5public.h closer to dev
byrnHDF Mar 3, 2021
35e1e68
Merges from develop
byrnHDF Mar 4, 2021
061da5f
format alignment
byrnHDF Mar 4, 2021
4f5536c
Add missing test ref file
byrnHDF Mar 4, 2021
84737cb
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Mar 5, 2021
a60c646
Merge #380 from develop
byrnHDF Mar 5, 2021
b0ee8ed
Finish java merges from develop
byrnHDF Mar 8, 2021
b6fd847
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Mar 8, 2021
24df8de
Fix java issues with tests and javadoc
byrnHDF Mar 9, 2021
7be7ae3
Correct use of attribute access plist
byrnHDF Mar 9, 2021
9c625d6
Remove debug code
byrnHDF Mar 9, 2021
754f639
Remove unused variable
byrnHDF Mar 9, 2021
b48feaf
Change file access to read only for java tests
byrnHDF Mar 9, 2021
655a5b1
Split clang format operations.
byrnHDF Mar 9, 2021
01e9241
More javadoc comments
byrnHDF Mar 9, 2021
ea5b297
Remove pre-split setting
byrnHDF Mar 10, 2021
0bd7344
format source
byrnHDF Mar 10, 2021
0c02446
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Mar 10, 2021
b6f6343
Change windows TS to use older VS.
byrnHDF Mar 10, 2021
d5fae65
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Mar 10, 2021
2e79275
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Mar 15, 2021
5c353c3
Mostly all javadoc fixes, one argument rename.
byrnHDF Mar 24, 2021
710cab2
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Mar 25, 2021
9c8f446
synch file
byrnHDF Mar 25, 2021
397bc7d
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Mar 31, 2021
df834ed
Merge of long double fix and compiler flags
byrnHDF Mar 31, 2021
6493701
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Apr 2, 2021
5fde49d
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Apr 5, 2021
c58432f
HDFFV-11229 merge changes from develop
byrnHDF Apr 5, 2021
ddd18c4
HDFFV-11229 correct test script
byrnHDF Apr 5, 2021
64b41eb
HDFFV-11229 update autotools test script for two ref files
byrnHDF Apr 5, 2021
aab960b
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Apr 7, 2021
93689e0
HDFFV-11229 merge dev changes for long double display in tools
byrnHDF Apr 7, 2021
5db53ab
Committing clang-format changes
github-actions[bot] Apr 7, 2021
df16379
minor whitespace
byrnHDF Apr 9, 2021
c5809ff
remove unneeded macro
byrnHDF Apr 15, 2021
39970a0
Merge branch 'hdf5_1_10' of https://github.com/byrnHDF/hdf5.git into …
byrnHDF Apr 15, 2021
1c73ec0
Committing clang-format changes
github-actions[bot] Apr 15, 2021
85e0d17
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Apr 20, 2021
e2329c4
Add "option" command for clang options
byrnHDF Apr 20, 2021
2aff5dd
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Apr 21, 2021
289ced6
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Apr 26, 2021
40cb29e
Rework CMake add_custom to use the BYPRODUCTS argument
byrnHDF Apr 28, 2021
7579264
Fortran target depends
byrnHDF Apr 28, 2021
ec8c003
Remove incorrect source attribute
byrnHDF Apr 28, 2021
b899fd2
Revert define removal
byrnHDF Apr 28, 2021
3a97a18
printf specifiers and VS2015 min changes
byrnHDF Apr 29, 2021
240277b
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Apr 29, 2021
ac82eb7
Committing clang-format changes
github-actions[bot] Apr 29, 2021
2ec49e0
Add time struct
byrnHDF Apr 29, 2021
6277997
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF Apr 30, 2021
ae7ea50
TRILAB-227 and tools debug merges from develop
byrnHDF May 7, 2021
e970984
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF May 18, 2021
79b03d3
Merge various changes from dev
byrnHDF May 19, 2021
9a95587
Issue #669 remove version from pkgcfg filename
byrnHDF May 21, 2021
006827c
remove version from h5cc script
byrnHDF May 21, 2021
7f5c5e9
Merge branch 'hdf5_1_10' of https://github.com/HDFGroup/hdf5.git into…
byrnHDF May 25, 2021
5dd2af9
doxygen changes merged from develop
byrnHDF May 25, 2021
7183953
Committing clang-format changes
github-actions[bot] May 25, 2021
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64 changes: 63 additions & 1 deletion MANIFEST
Original file line number Diff line number Diff line change
Expand Up @@ -206,13 +206,74 @@

./doxygen/aliases
./doxygen/Doxyfile.in
./doxygen/dox/About.dox
./doxygen/dox/Cookbook.dox
./doxygen/dox/DDLBNF110.dox
./doxygen/dox/FileFormatSpec.dox
./doxygen/dox/GettingStarted.dox
./doxygen/dox/H5AC_cache_config_t.dox
./doxygen/dox/H5Acreate.dox
./doxygen/dox/H5Aiterate.dox
./doxygen/dox/H5Fget_info.dox
./doxygen/dox/H5Lget_info_by_idx.dox
./doxygen/dox/H5Lget_info.dox
./doxygen/dox/H5Literate_by_name.dox
./doxygen/dox/H5Literate.dox
./doxygen/dox/H5Lvisit_by_name.dox
./doxygen/dox/H5Lvisit.dox
./doxygen/dox/H5Oget_info_by_idx.dox
./doxygen/dox/H5Oget_info_by_name.dox
./doxygen/dox/H5Oget_info.dox
./doxygen/dox/H5Ovisit_by_name.dox
./doxygen/dox/H5Ovisit.dox
./doxygen/dox/H5Sencode.dox
./doxygen/dox/MetadataCachingInHDF5.dox
./doxygen/dox/OtherSpecs.dox
./doxygen/dox/Overview.dox
./doxygen/dox/ReferenceManual.dox
./doxygen/dox/Specifications.dox
./doxygen/dox/TechnicalNotes.dox
./doxygen/dox/api-compat-macros.dox
./doxygen/dox/mainpage.dox
./doxygen/dox/maybe_metadata_reads.dox
./doxygen/dox/rm-template.dox
./doxygen/examples/FF-IH_FileGroup.gif
./doxygen/examples/FF-IH_FileObject.gif
./doxygen/examples/FileFormatSpecChunkDiagram.jpg
./doxygen/examples/H5Pset_metadata_read_attempts.c
./doxygen/examples/H5Pset_object_flush_cb.c
./doxygen/examples/H5.format.1.0.html
./doxygen/examples/H5.format.1.1.html
./doxygen/examples/H5.format.2.0.html
./doxygen/examples/H5.format.html
./doxygen/examples/H5A_examples.c
./doxygen/examples/H5D_examples.c
./doxygen/examples/H5Fclose.c
./doxygen/examples/H5Fcreate.c
./doxygen/examples/H5F_examples.c
./doxygen/examples/H5Pget_metadata_read_attempts.1.c
./doxygen/examples/H5Pget_metadata_read_attempts.2.c
./doxygen/examples/H5Pget_metadata_read_attempts.3.c
./doxygen/examples/H5Pget_object_flush_cb.c
./doxygen/examples/ImageSpec.html
./doxygen/examples/PaletteExample1.gif
./doxygen/examples/Palettes.fm.anc.gif
./doxygen/examples/TableSpec.html
./doxygen/examples/ThreadSafeLibrary.html
./doxygen/examples/VFL.html
./doxygen/examples/hello_hdf5.c
./doxygen/hdf5_footer.html
./doxygen/hdf5_header.html
./doxygen/hdf5_navtree_hacks.js
./doxygen/hdf5doxy.css
./doxygen/hdf5doxy_layout.xml
./doxygen/img/FF-IH_FileGroup.gif
./doxygen/img/FF-IH_FileObject.gif
./doxygen/img/FileFormatSpecChunkDiagram.jpg
./doxygen/img/HDFG-logo.png
./doxygen/img/PaletteExample1.gif
./doxygen/img/Palettes.fm.anc.gif
./doxygen/img/ftv2node.png
./doxygen/img/ftv2pnode.png

./examples/Attributes.txt
./examples/Makefile.am
Expand Down Expand Up @@ -548,6 +609,7 @@
./src/H5err.txt
./src/H5detect.c
./src/H5make_libsettings.c
./src/H5module.h
./src/H5mpi.c
./src/H5overflow.txt
./src/H5private.h
Expand Down
27 changes: 23 additions & 4 deletions configure.ac
Original file line number Diff line number Diff line change
Expand Up @@ -1089,18 +1089,37 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
AC_SUBST([DOXYGEN_OPTIMIZE_OUTPUT_FOR_C])
AC_SUBST([DOXYGEN_MACRO_EXPANSION])
AC_SUBST([DOXYGEN_OUTPUT_DIRECTORY])

AC_SUBST([DOXYGEN_EXAMPLES_DIRECTORY])
AC_SUBST([DOXYGEN_LAYOUT_FILE])
AC_SUBST([DOXYGEN_HTML_HEADER])
AC_SUBST([DOXYGEN_HTML_FOOTER])
AC_SUBST([DOXYGEN_HTML_EXTRA_STYLESHEET])
AC_SUBST([DOXYGEN_HTML_EXTRA_FILES])
AC_SUBST([DOXYGEN_SERVER_BASED_SEARCH])
AC_SUBST([DOXYGEN_EXTERNAL_SEARCH])
AC_SUBST([DOXYGEN_SEARCHENGINE_URL])

# SRCDIR Environment variables used inside doxygen macro for the source location:
DOXYGEN_PACKAGE=${PACKAGE_NAME}
DOXYGEN_VERSION_STRING=${PACKAGE_VERSION}
DOXYGEN_INCLUDE_ALIASES='$(SRCDIR)/doxygen/aliases'
DOXYGEN_PROJECT_LOGO='$(SRCDIR)/doxygen/img/HDFG-logo.png'
DOXYGEN_PROJECT_BRIEF="C-API Reference"
DOXYGEN_PROJECT_BRIEF=
DOXYGEN_INPUT_DIRECTORY='$(SRCDIR) $(SRCDIR)/doxygen/dox'
DOXYGEN_OPTIMIZE_OUTPUT_FOR_C=YES
DOXYGEN_MACRO_EXPANSION=YES
DOXYGEN_OUTPUT_DIRECTORY=hdf5lib_docs

DX_INIT_DOXYGEN([HDF5], [../doxygen/Doxyfile], [hdf5lib_docs])
DOXYGEN_EXAMPLES_DIRECTORY='$(SRCDIR)/doxygen/examples $(SRCDIR)/src $(SRCDIR)/examples $(SRCDIR)/test'
DOXYGEN_LAYOUT_FILE='$(SRCDIR)/doxygen/hdf5doxy_layout.xml'
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_SERVER_BASED_SEARCH=NO
DOXYGEN_EXTERNAL_SEARCH=NO
DOXYGEN_SEARCHENGINE_URL=

DX_INIT_DOXYGEN([HDF5], [./doxygen/Doxyfile], [hdf5lib_docs])

else
AC_MSG_RESULT([no])
Expand Down
39 changes: 23 additions & 16 deletions doxygen/Doxyfile.in
Original file line number Diff line number Diff line change
Expand Up @@ -738,7 +738,7 @@ FILE_VERSION_FILTER =
# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
# tag is left empty.

LAYOUT_FILE =
LAYOUT_FILE = @DOXYGEN_LAYOUT_FILE@

# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
# the reference definitions. This must be a list of .bib files. The .bib
Expand Down Expand Up @@ -855,9 +855,16 @@ INPUT_ENCODING = UTF-8

FILE_PATTERNS = H5*public.h \
H5*module.h \
H5VLconnector.h \
H5VLconnector_passthru.h \
H5VLnative.h \
H5FDcore.h \
H5FDdirect.h \
H5FDfamily.h \
H5FDlog.h \
H5FDmpi.h \
H5FDmpio.h \
H5FDmulti.h \
H5FDsec2.h \
H5FDstdio.h \
H5FDwindows.h \
H5version.h \
*.dox

Expand Down Expand Up @@ -907,7 +914,7 @@ EXCLUDE_SYMBOLS =
# that contain example code fragments that are included (see the \include
# command).

EXAMPLE_PATH = ../src ../examples ../test examples
EXAMPLE_PATH = @DOXYGEN_EXAMPLES_DIRECTORY@

# If the value of the EXAMPLE_PATH tag contains directories, you can use the
# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
Expand Down Expand Up @@ -1168,7 +1175,7 @@ HTML_FILE_EXTENSION = .html
# of the possible markers and block names see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.

HTML_HEADER =
HTML_HEADER = @DOXYGEN_HTML_HEADER@

# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
# generated HTML page. If the tag is left blank doxygen will generate a standard
Expand All @@ -1178,7 +1185,7 @@ HTML_HEADER =
# that doxygen normally uses.
# This tag requires that the tag GENERATE_HTML is set to YES.

HTML_FOOTER =
HTML_FOOTER = @DOXYGEN_HTML_FOOTER@

# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
# sheet that is used by each HTML page. It can be used to fine-tune the look of
Expand All @@ -1203,7 +1210,7 @@ HTML_STYLESHEET =
# list). For an example see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.

HTML_EXTRA_STYLESHEET =
HTML_EXTRA_STYLESHEET = @DOXYGEN_HTML_EXTRA_STYLESHEET@

# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
# other source files which should be copied to the HTML output directory. Note
Expand All @@ -1213,7 +1220,7 @@ HTML_EXTRA_STYLESHEET =
# files will be copied as-is; there are no commands or markers available.
# This tag requires that the tag GENERATE_HTML is set to YES.

HTML_EXTRA_FILES =
HTML_EXTRA_FILES = @DOXYGEN_HTML_EXTRA_FILES@

# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
# will adjust the colors in the style sheet and background images according to
Expand Down Expand Up @@ -1271,7 +1278,7 @@ HTML_DYNAMIC_MENUS = NO
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.

HTML_DYNAMIC_SECTIONS = NO
HTML_DYNAMIC_SECTIONS = YES

# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
# shown in the various tree structured indices initially; the user can expand
Expand Down Expand Up @@ -1483,7 +1490,7 @@ ECLIPSE_DOC_ID = org.doxygen.Project
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.

DISABLE_INDEX = NO
DISABLE_INDEX = YES

# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
# structure should be generated to display hierarchical information. If the tag
Expand Down Expand Up @@ -1631,7 +1638,7 @@ MATHJAX_CODEFILE =
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.

SEARCHENGINE = NO
SEARCHENGINE = YES

# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
# implemented using a web server instead of a web client using JavaScript. There
Expand All @@ -1643,7 +1650,7 @@ SEARCHENGINE = NO
# The default value is: NO.
# This tag requires that the tag SEARCHENGINE is set to YES.

SERVER_BASED_SEARCH = YES
SERVER_BASED_SEARCH = @DOXYGEN_SERVER_BASED_SEARCH@

# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
# script for searching. Instead the search results are written to an XML file
Expand All @@ -1659,7 +1666,7 @@ SERVER_BASED_SEARCH = YES
# The default value is: NO.
# This tag requires that the tag SEARCHENGINE is set to YES.

EXTERNAL_SEARCH = NO
EXTERNAL_SEARCH = @DOXYGEN_EXTERNAL_SEARCH@

# The SEARCHENGINE_URL should point to a search engine hosted by a web server
# which will return the search results when EXTERNAL_SEARCH is enabled.
Expand All @@ -1670,7 +1677,7 @@ EXTERNAL_SEARCH = NO
# Searching" for details.
# This tag requires that the tag SEARCHENGINE is set to YES.

SEARCHENGINE_URL =
SEARCHENGINE_URL = @DOXYGEN_SEARCHENGINE_URL@

# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
# search data is written to a file for indexing by an external tool. With the
Expand Down Expand Up @@ -2167,7 +2174,7 @@ INCLUDE_FILE_PATTERNS =
# recursively expanded use the := operator instead of the = operator.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.

PREDEFINED =
PREDEFINED = H5_HAVE_PARALLEL

# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
# tag can be used to specify a list of macro names that should be expanded. The
Expand Down
39 changes: 36 additions & 3 deletions doxygen/aliases
Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
ALIASES += THG="The HDF Group"

################################################################################
# Styling
################################################################################
Expand Down Expand Up @@ -35,6 +37,9 @@ 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"

################################################################################
# Attributes
################################################################################
Expand All @@ -60,12 +65,19 @@ ALIASES += space_id{1}="\param[in] \1 Dataspace identifier"
# Dataypes
################################################################################

ALIASES += dtype_id="\param[in] dtype_id Datatype identifier"
ALIASES += dtype_id{1}="\param[in] \1 Datatype identifier"
ALIASES += type_id="\param[in] type_id Datatype identifier"
ALIASES += type_id{1}="\param[in] \1 Datatype identifier"

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
################################################################################
Expand Down Expand Up @@ -160,11 +172,32 @@ ALIASES += fgdta_loc_obj_id{1}="\loc_obj_id{\1}. The identifier may be that of a

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_110="<a href=\"https://portal.hdfgroup.org/display/HDF5/New+Features+in+HDF5+Release+1.10\">New Features in HDF5 Release 1.10</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>"
Expand All @@ -180,5 +213,5 @@ 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>"
11 changes: 11 additions & 0 deletions doxygen/dox/About.dox
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/** \page About About

The implementation of this documentation set is based on the fantastic work of the
<a href="https://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen project</a>.
Please refer to their <a href="https://gitlab.com/libeigen/eigen">GitLab repository</a>
and the online version of their
<a href="http://eigen.tuxfamily.org/dox/">Doxygen-based documentation</a>.
Not only does Eigen set a standard as a piece of software, but also as an example
of <em>documentation done right</em>.

*/
5 changes: 5 additions & 0 deletions doxygen/dox/Cookbook.dox
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/** \page Cookbook Cookbook

Healthy, everyday recipes for every taste and budget...

*/
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