Merge doxygen2 into develop (#553)

* Fixed warnings and started H5Epublic.h.

* Include H5FD* headers to correctly resolve references.

* Doxygen2 (#330)

* H5Eauto_is_v2.

* Added a few more calls.

* Added a few more H5E calls.

* First cut of H5E v2.

* Added the deprecated v1 calls.

* Updated spacing.

* Once more.

* Taking some inspiration from Eigen3.

* Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pen… (#352)

* Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pencode1, H5Pget_filter_by_id1,H5Pget_version, H5Pset_file_space,H5Pget_file_space. Someone already adds H5Pget_filter1. Also fixs an extra parameter 'close' call back function for HPregister2.

* doxygen work. fixs format by using clang-format.

* doxgen work for H5Pregister1 etc. Addressed Barbara and Gerd's comments.
For Quincey's comments, since we are not supposed to change the source code.
I leave this to future improvements.

* added documentation for H5P APIs (#350)

* add documenation for H5Pget_buffer,H5Pget_data_transform,H5Pget_edc_check,H5Pget_hyper_vector_size,H5Pget_preserve,H5Pget_type_conv_cb,H5Pget_vlen_mem_manager,H5Pset_btree_ratios

* format corrections

* fixed grammer

* fixed herr_t

* Better name.

* A fresh look.

* add doxygen to H5Ppublic.h

* use attention instead of warning

* Add doxygen comments in H5Ppublic.h (#375)

* Add doxygen comments in H5Ppublic.h

* H5Pset_meta_block_size
* H5Pset_metadata_read_attempts
* H5Pset_multi_type
* H5Pset_object_flush_cb
* H5Pset_sieve_buf_size
* H5Pset_small_data_block_size
* H5Pset_all_coll_metadata_ops
* H5Pget_all_coll_metadata_ops

* Add DOXYGEN_EXAMPLES_DIR to src/CMakeLists.txt

* Fix clang-format errors

* Fix filenames in doxygen/examples

* add doxygen to H5Ppublic.h (#378)

* add doxygen to H5Ppublic.h

* use attention instead of warning

Co-authored-by: Kimmy Mu <kmu@hdfgroup.org>

* Revert "add doxygen to H5Ppublic.h (#378)"

This reverts commit 2ee1821b138a5c00b15ea57ce9e950367480f5f2.

* Updated Doxygen variables.

* I forgot to copy two images.

* Enable desktop search by default.

* Add my assigned Doxygen documentation.

* Remove whitespace at EOL.  Appease clang-format.

* Addressed Chris' comments.

* Added an alias for asynchronous functions.

* One space is enough for all of us.

* Slightly restructured RM page.

* address some issues

* reformatting

* Style external links.

* reformatting

* reformatting

* Added "Metadata Caching in HDF5" as a technical note example.

* Revise this soon!

* Added specification examples.

* Fixed references.

* Added H5AC cache image stuff and file format study.

* Added older FMT versions. Where did 1.0 go?

* Updated C/C++ note and replaced ambiguous labels.

* Reformat source with clang v10.0.1.

* Added the VFL technical note.

* Added what I believe might be called version 1.0 of the format.

* Added the remaining specs.

* Added H5Z callback documentation and fixed a few mistakes.

* Added dox for deprecated H5G calls and fixed a few snippet blockIDs.

* clang-format happy?

* Ok?

* Bonus track: Deprecated H5D functions.

* Carry over the more detailed group description.

* Added documentation for the missing and deprecated H5R calls.

* Life is easier and less repetitive w/ snippets. Use them!

* Eliminate the snippet block ID artifacts in the HTML rendering.

* Fixed snippet HTML artifacts and added a few missing calls.

* Under 20 H5Ps to go!

* Almost complete!

* "This is a form of pedantry up with which I will not put." (Churchill)

* Let's not waste as much space on bulleted lists!

* First complete (?) draft of the Doxygen-based RM.

* Completeness check and minor fixes along the way.

* Pedantry.

* Adding missing H5FD calls checkpoint.

* Pedantry.

* More pedantry.

* Added H5Pset_fapl_log.

* First draft of H5ES.

* Fixed warnings.

* Prep. for map module.

* First cut of the map module.

* Pedantry.

* Possible H5F introduction.

* Fix the indentation.

* Pedantry.

* Ditto.

* Thanks to the reviewers for their comments.

* Added missing images.

* Line numbers are a distraction here.

* More examples, references, and clean-up. Don't repeat yourself!

* Clang pedantry.

* Ditto.

* More reviewer comments...

* Templatized references and cleaned up \todos.

* Committing clang-format changes

* Fixed MANIFEST.

* Addressed Quincey's comments. (OCPLs)

* Fixed a few more \todo items.

* Fixed more \todo items.

* Added attribute life cycle.

* Forgot the examples file.

* Committing clang-format changes

* Pedantry.

* Live and learn!

* Added a sample H5D life cycle.

* Committing clang-format changes

* Pedantry.

Co-authored-by: kyang2014 <kyang2014@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>
Co-authored-by: Kimmy Mu <kmu@hdfgroup.org>
Co-authored-by: Christopher Hogan <ChristopherHogan@users.noreply.github.com>
Co-authored-by: jya-kmu <53388330+jya-kmu@users.noreply.github.com>
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

1 files changed, 48 insertions, 2 deletions

diff --git a/MANIFEST b/MANIFEST
index 9b0ce1c..f7a4983 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -207,7 +207,12 @@
 
 ./doxygen/aliases
 ./doxygen/Doxyfile.in
-./doxygen/dox/api-compat-macros.dox
+./doxygen/dox/About.dox
+./doxygen/dox/Cookbook.dox
+./doxygen/dox/DDLBNF110.dox
+./doxygen/dox/DDLBNF112.dox
+./doxygen/dox/FileFormatSpec.dox
+./doxygen/dox/GettingStarted.dox
 ./doxygen/dox/H5AC_cache_config_t.dox
 ./doxygen/dox/H5Acreate.dox
 ./doxygen/dox/H5Aiterate.dox
@@ -224,12 +229,53 @@
 ./doxygen/dox/H5Ovisit_by_name.dox
 ./doxygen/dox/H5Ovisit.dox
 ./doxygen/dox/H5Sencode.dox
-./doxygen/dox/mainpage.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/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