Hdf5 1 8 doxygen merges (#683)

* Update supported platforms

* Merge PR#3 changes from develop

* # WARNING: head commit changed in the meantime

Merge gcc 10 diagnostics option from develop

Merge CMake changes from develop
Merge warnings from develop
Merge #318 OSX changes from develop
Merge tools changes from develop
Merge test macros from develop

* Format updates

* Fix missing semicolon and format fix

* Format update

* Correct actions, remove java option

* Update autotools build files

* Add testfiles

* Fix configure issue with make flags

* Init fapls to default

* Update generated files and fix h5repack id closure

* update format

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
whitespace cleanup
tools sync

* format alignment

* initialize vars

* revert H5private change

* Merge #380 from develop

* Split format source and commit changes on repo push

* Change windows TS to use older VS.

* HDFFV-11229 merge dev changes for long double display in tools

* Committing clang-format changes

* Update unsupported types with precision

* Add "option" command for clang options

* CMake merges from develop h5cc scripts

* Updates from develop and printf formatters

* Committing clang-format changes

* Issue #669 remove version from pkgcfg filename

* remove version from h5cc script

* doxygen changes merged from develop

* Committing clang-format changes

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

MANIFEST

@@ -196,13 +196,60 @@
 
 ./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/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/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

doxygen/aliases

@@ -195,5 +195,4 @@ 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>"

doxygen/dox/About.dox

@@ -0,0 +1,11 @@
+/** \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>.
+
+*/

doxygen/dox/Cookbook.dox

@@ -0,0 +1,5 @@
+/** \page Cookbook Cookbook
+
+ Healthy, everyday recipes for every taste and budget...
+
+ */