hdf5/doxygen/dox/About.dox

127 lines
5.1 KiB
Plaintext
Raw Normal View History

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>
2021-04-27 03:07:29 +08:00
/** \page About About
\section about_history History
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>
2021-04-27 03:07:29 +08:00
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>.
\section about_documentation Documentation about Documentation
Next batch of Doxygen updates. (#1180) * Sketch of the H5S life cycle. * Committing clang-format changes * Fix H5S_UNLIMITED snafu. * Updated RM template and RM page. * Added H5S life cycle. * Committing clang-format changes * Added H5T life cycle. * Committing clang-format changes * Cleaner layout (?) * Cleaned the H5F life cycle. Called out unfinished biz. * Committing clang-format changes * Remaining life cycle skeletons. * Committing clang-format changes * Committing clang-format changes * Added H5Z life cycle. * Committing clang-format changes * Added H5G life cycle. * Committing clang-format changes * H5 and H5I life cycle updates. * Committing clang-format changes * Added H5PL life cycle. * Committing clang-format changes * Added H5L life cycle. * Committing clang-format changes * Fix for Chris' comment. * Add a variable for Doxygen pre-processor definitions. * Forgot to add the H5M API. * Clarify the H5Z life cycle. * Committing clang-format changes * Add H5Zdevelop.h to Doxygen.in. Added H5I life cycle. * Committing clang-format changes * Clarified introduction and fixed missing label declaration. * Added H5O life cycle. * Committing clang-format changes * H5O cleanup, part 1. * Committing clang-format changes * Cleaned up some of the endless repetition in H5O. * Committing clang-format changes * Cookbook & RFC draft layouts. * Updated manifest. * Updated the manifest, the example paths, and sketched the 1st recipe. * Committing clang-format changes * Outlined two more recipes. * Committing clang-format changes * More recipes and RFCs. * Committing clang-format changes * Draft of templatized RFC references. * Another batch of RFC changes. * Another batch of RFCs. * Fixed reference. * RFCs in reverse chronological order. * First cut of RFCs. * Fixed reference. * Updated recipes. * Updated recipes. * More RFCs. * Updated D*PL comments. * Added H5P descriptions. * Committing clang-format changes * H5R life-cycle snapshot. * Committing clang-format changes * H5R life-cycle. Added line numbers to life-cycle examples. * Committing clang-format changes * Fixed formatting for H5Dchunk_iter(). * Added comment on collective mode requirement w/ compression. * Simplified API compat. macro dox. * More API vers. updates. * Hide the async macro entrails. * Latest VFD SWMR RFC. * Create a tag file for permalinks. * Added TODOs for metadoc. * Removed duplication. * Revised RM landing page. * Trimmed more duplication. * Committing clang-format changes * Revised H5D. * Committing clang-format changes * Updated survey link. * Added Doxygen RM entry template link. * Added the "Multi-Thread HDF5" RFC. * Added DOXYGEN_TAG_FILE. * Added selection I/O RFC. * Added the VFD Sub-filing RFC. * Updated meta-documentation and added two old presentations. * Added a few more RFCs (4). * Fixed MANIFEST. * Updated meta-documentation. * Added Filters technical note. * Fixed MANIFEST. * Restore the path stripper. * Experimental full-text search via Google. * Better full-text search integration. * Whoops. Forgot this one. * Oh boy. * Make CMake happy. * Added "Debugging HDF5 Applications" technical note. * Another batch of RFCs. Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
2021-11-23 22:05:40 +08:00
In this section, we describe common documentation maintenance tasks.
\subsection plain_html Including Plain HTML Pages
The most common use case for this is the inclusion of older documentation.
New documentation should, whenever possible, be created using Doxygen markdown!
Use Doxygen's <a href="https://www.doxygen.nl/manual/commands.html#cmdhtmlinclude"><code>htmlinclude</code></a>
special command to include existing plain HTML pages.
An example from this documentation set can be seen
<a href="https://github.com/HDFGroup/hdf5/blob/develop/doxygen/dox/FileFormatSpec.dox">here</a>.
\subsection new_rm_entry Creating a New Reference Manual Entry
Please refer to the \ref RMT for guidance on how to create a new reference manual entry.
\subsubsection new_example Adding and Referencing API Examples
For each HDF5 module, such as \Code{H5F}, there is an examples source file called
\Code{H5*_examples.c}. For example, the \Code{H5F} API examples are located in
<a href="https://github.com/HDFGroup/hdf5/blob/develop/doxygen/examples/H5F_examples.c">
<code>H5F_examples.c</code></a>. Examples are code blocks marked as Doxygen
<a href="https://www.doxygen.nl/manual/commands.html#cmdsnippet">snippets</a>.
For example, the source code for the H5Fcreate() API sample is located between
the
\verbatim
//! <!-- [create] -->
...
//! <!-- [create] -->
\endverbatim
comments in
<a href="https://github.com/HDFGroup/hdf5/blob/develop/doxygen/examples/H5F_examples.c">
<code>H5F_examples.c</code></a>.
Add a new API example by adding a new code block enclosed between matching
snippet tags. The name of the tag is usually the function name stripped of
the module prefix.
The inclusion of such a block of code can then be triggered via Doxygen's
<a href="https://www.doxygen.nl/manual/commands.html#cmdsnippet"><code>snippet</code></a>
special command. For example, the following markup
\verbatim
* \snippet H5F_examples.c create
\endverbatim
yields
\snippet H5F_examples.c create
\subsubsection api_macro Adding an API Macro
API macros are handled by the <code>api_vers_2, api_vers_3, api_vers_4</code>
custom commands. The numbers indicate the number of potential API function
mappings. For example, H5Acreate() has two potential mappings, H5Acreate1() and
H5Acreate2(). To trigger the creation of a reference manual entry for H5Acreate()
use the following markup:
\verbatim
\api_vers_2{H5Acreate,H5Acreate1,H5Acreate2}
\endverbatim
This yields:
\api_vers_2{H5Acreate,H5Acreate1,H5Acreate2}
\subsection custom_commands Creating Custom Commands
See Doxygen's <a href="https://www.doxygen.nl/manual/custcmd.html">Custom Commands documentation</a>
as a general reference.
All custom commands for this project are located in the
<a href="https://github.com/HDFGroup/hdf5/blob/develop/doxygen/aliases"><tt>aliases</tt></a>
file in the <a href="https://github.com/HDFGroup/hdf5/tree/develop/doxygen"><tt>doxygen</tt></a>
subdirectory of the <a href="https://github.com/HDFGroup/hdf5">main HDF5 repo</a>.
The custom commands are grouped in sections. Find a suitable section for your command or
ask for help if unsure!
\subsection new_rfc Adding a New RFC or Referencing an Existing RFC
For ease of reference, we define custom commands for each RFC in the <tt>RFCs</tt> section
of the
<a href="https://github.com/HDFGroup/hdf5/blob/develop/doxygen/aliases"><tt>aliases</tt></a>
file. For example the custom command \Code{ref_rfc20141210} can be used to insert a
reference to "RFC: Virtual Object Layer". In other words, the markup
\verbatim
\ref_rfc20141210
\endverbatim
yields a clickable link:
\ref_rfc20141210
To add a new RFC, add a custom command for the RFC to the
<a href="https://github.com/HDFGroup/hdf5/blob/develop/doxygen/aliases"><tt>aliases</tt></a>
file. The naming convention for the custom command is \Code{ref_rfcYYYYMMDD},
where \Code{YYYYMMDD} is the ID of the RFC. The URL is composed of the prefix
\verbatim
https://docs.hdfgroup.org/hdf5/rfc/
\endverbatim
and the name of your RFC file, typically, a PDF file, i.e., the full URL would
be
\verbatim
https://docs.hdfgroup.org/hdf5/rfc/my_great_rfc_name.pdf
\endverbatim
\subsection hosting How Do Updates and Changes Get Published?
Currently, the files underlying this documentation website are stored in an
bucket on AWS S3. The top-level bucket is <pre>s3://docs.hdfgroup.org/hdf5/</pre>
There are folders for the <tt>development</tt> branch and all supported release
version.
Talk to your friendly IT-team if you need write access, or you need someone to
push an updated version for you!
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>
2021-04-27 03:07:29 +08:00
*/