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, 193 insertions, 0 deletions

diff --git a/doxygen/examples/TableSpec.html b/doxygen/examples/TableSpec.html
new file mode 100644
index 0000000..474176e
--- /dev/null
+++ b/doxygen/examples/TableSpec.html
@@ -0,0 +1,193 @@
+<html>
+<head>
+   <title>HDF5 Table Specification</title>
+</head>
+
+The HDF5 specification defines the standard objects and storage for the
+standard HDF5 objects. (For information about the HDF5 library, model and
+specification, see the HDF documentation.)&nbsp; This document is an additional
+specification do define a standard profile for how to store tables in HDF5.
+Table data in HDF5 is stored as HDF5 datasets with standard attributes to define
+the properties of the tables.
+
+<h2>
+1. Overview</h2>
+A generic table is a sequence of records, each record has a name and a type.
+Table data is stored as an HDF5 one dimensional compound dataset.&nbsp; A table
+is defined as a collection of records whose values are stored in fixed-length
+fields. All records have the same structure and all values in each field have
+the same data type.
+<p>The dataset for a table is distinguished from other datasets by giving
+it an attribute &quot;CLASS=TABLE&quot;.&nbsp;&nbsp;
+Optional attributes allow the storage of a title for the Table and for
+each column, and a fill value for each column.
+<h2>
+2.&nbsp; Table Attributes</h2>
+The attributes for the Table are strings.&nbsp;They are written with the <a href="RM_H5LT.html#H5LTset_attribute_string"><code>H5LTset_attribute_string</code></a>
+Lite API function.&nbsp; "Required" attributes must always be used. "Optional" attributes
+must be used when required.
+<br>&nbsp;
+<h4>
+Attributes</h4>
+
+<dl>
+<dt>
+Attribute name="<b>CLASS</b>" (Required)</dt>
+
+<dd>
+This attribute is type H5T_C_S1, with size 5.</dd>
+
+<dd>
+For all Tables, the value of this attribute is &quot;TABLE&quot;.</dd>
+
+<dd>
+This attribute identifies this data set as intended to be interpreted as Table that conforms to the specifications on this page.</dd>
+</dl>
+
+<dl>
+Attribute name="<b>VERSION</b>" (Required)
+
+<dd>
+This attribute is of type H5T_C_S1, with size corresponding to the length
+of the version string.&nbsp; This attribute identifies the version number
+of this specification to which it conforms.&nbsp; The current version number
+is &quot;0.2&quot;.</dd>
+
+</dl>
+
+<dl>
+<dt>
+Attribute name="<b>TITLE</b>" (Optional)</dt>
+
+<dd>
+The <b>TITLE</b> is an optional String that is to be used as the
+informative title of the whole table.
+The <b>TITLE</b> is set with the parameter <code> table_title</code> of the function
+<a href="RM_H5TB.html#H5TBmake_table"> <code> H5TBmake_table</code></a>.&nbsp;</dd>
+</dl>
+
+<dl>
+<dt>
+Attribute name="<b>FIELD_(n)_NAME</b>" (Required)</dt>
+
+<dd>
+The <b>FIELD_(n)_NAME</b> is an optional String that is to be used as the
+informative title of column <b>n</b> of the table.
+For each of the fields the word FIELD_ is concatenated with
+      the zero based field (n) index together with the name of the field.</dd>
+
+</dl>
+<dl>
+<dt>
+Attribute name="<b>FIELD_(n)_FILL</b>" (Optional)</dt>
+
+<dd>
+The <b>FIELD_(n)_FILL</b> is an optional String that is the fill value for
+column <b>n</b> of the table.
+For each of the fields the word FIELD_ is concatenated with
+      the zero based field (n) index together with the fill value, if present.
+This value is written only when a fill value is defined for the table.</dd>
+
+</dl>
+
+<dl>
+
+<br>&nbsp;
+<center><table BORDER=2 BGCOLOR="#FFFFFF" >
+<caption><b>Table 1. Attributes of an Image Dataset</b></caption>
+
+<tr>
+<td><b>Attribute Name</b></td>
+
+<td><b>(R = Required</b>
+<br><b>O= Optional)</b></td>
+
+<td><b>Type</b></td>
+
+<td><b>String Size</b></td>
+
+<td><b>Value</b></td>
+</tr>
+
+<tr>
+<td>CLASS</td>
+
+<td>R</td>
+
+<td>String</td>
+
+<td>5</td>
+
+<td>&quot;TABLE&quot;</td>
+</tr>
+
+<tr>
+<td>VERSION</td>
+
+<td>R</td>
+
+<td>String</td>
+
+<td>3</td>
+
+<td>&quot;0.2&quot;</td>
+</tr>
+
+<tr>
+<td>TITLE</td>
+
+<td>O</td>
+
+<td>String</td>
+
+<td>&nbsp;</td>
+
+<td>
+
+<tr>
+<td>FIELD_(n)_NAME</td>
+
+<td>R</td>
+
+<td>String</td>
+
+<td>&nbsp;</td>
+
+<td>
+&nbsp;
+
+<tr>
+<td>FIELD_(n)_FILL</td>
+
+<td>O*</td>
+
+<td>String</td>
+
+<td>&nbsp;</td>
+
+<td>
+&nbsp;
+</table>
+</center>
+
+  </dl>
+<p>
+<center>
+&nbsp;
+</center>
+<i>* </i>The attribute FIELD_(n)_FILL is written to the table if a fill value is
+specified on the creation of the Table. Otherwise, it is not.<p>The following
+section of code shows the calls necessary to the creation of a table.
+
+<p><code>/* Create a new HDF5 file using default properties. */<br>
+ file_id = H5Fcreate( &quot;my_table.h5&quot;, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );</code> </p>
+
+<p><code>/* Call the make table function */<br>
+</code> <code>H5TBmake_table( "Table Title", file_id, "Table1", NFIELDS, NRECORDS, dst_size,&nbsp;<br>
+                       field_names, dst_offset, field_type,&nbsp;<br>
+                       chunk_size, fill_data, compress, p_data  )&nbsp;</code> </p>
+
+<p><code> /* Close the file. */<br>
+ status = H5Fclose( file_id );</code> </p>
+
+</body>