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, 62 insertions, 1 deletions

diff --git a/src/H5FDdirect.h b/src/H5FDdirect.h
index eec10de..f06de7f 100644
--- a/src/H5FDdirect.h
+++ b/src/H5FDdirect.h
@@ -37,8 +37,69 @@ extern "C" {
 #define FBSIZE_DEF    4096
 #define CBSIZE_DEF    16 * 1024 * 1024
 
-H5_DLL hid_t  H5FD_direct_init(void);
+H5_DLL hid_t H5FD_direct_init(void);
+
+/**
+ * \ingroup FAPL
+ *
+ * \brief Sets up use of the direct I/O driver
+ *
+ * \fapl_id
+ * \param[in] alignment Required memory alignment boundary
+ * \param[in] block_size File system block size
+ * \param[in] cbuf_size Copy buffer size
+ * \returns \herr_t
+ *
+ * \details H5Pset_fapl_direct() sets the file access property list, \p fapl_id,
+ *          to use the direct I/O driver, #H5FD_DIRECT. With this driver, data
+ *          is written to or read from the file synchronously without being
+ *          cached by the system.
+ *
+ *          File systems usually require the data address in memory, the file
+ *          address, and the size of the data to be aligned. The HDF5 library’s
+ *          direct I/O driver is able to handle unaligned data, though that will
+ *          consume some additional memory resources and may slow
+ *          performance. To get better performance, use the system function \p
+ *          posix_memalign to align the data buffer in memory and the HDF5
+ *          function H5Pset_alignment() to align the data in the file. Be aware,
+ *          however, that aligned data I/O may cause the HDF5 file to be bigger
+ *          than the actual data size would otherwise require because the
+ *          alignment may leave some holes in the file.
+ *
+ *          \p alignment specifies the required alignment boundary in memory.
+ *
+ *          \p block_size specifies the file system block size. A value of 0
+ *          (zero) means to use HDF5 library’s default value of 4KB.
+ *
+ *          \p cbuf_size specifies the copy buffer size.
+ *
+ * \since 1.8.0
+ *
+ */
 H5_DLL herr_t H5Pset_fapl_direct(hid_t fapl_id, size_t alignment, size_t block_size, size_t cbuf_size);
+
+/**
+ * \ingroup FAPL
+ *
+ * \brief Retrieves direct I/O driver settings
+ *
+ * \fapl_id
+ * \param[out] boundary Required memory alignment boundary
+ * \param[out] block_size File system block size
+ * \param[out] cbuf_size Copy buffer size
+ * \returns \herr_t
+ *
+ * \details H5Pget_fapl_direct() retrieves the required memory alignment (\p
+ *          alignment), file system block size (\p block_size), and copy buffer
+ *          size (\p cbuf_size) settings for the direct I/O driver, #H5FD_DIRECT,
+ *          from the file access property list \p fapl_id.
+ *
+ *          See H5Pset_fapl_direct() for discussion of these values,
+ *          requirements, and important considerations.
+ *
+ * \since 1.8.0
+ *
+ */
 H5_DLL herr_t H5Pget_fapl_direct(hid_t fapl_id, size_t *boundary /*out*/, size_t *block_size /*out*/,
                                  size_t *cbuf_size /*out*/);