Update secondary file on compression, referenced by other file.

HDFGroup · Jan 8, 2025 · 5e91f0e · 5e91f0e
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diff --git a/doxygen/aliases b/doxygen/aliases
@@ -257,6 +257,13 @@ ALIASES += callback_note="\attention \Bold{Leaving callback functions:}\n The ca
 ALIASES += par_compr_note="\attention If you are planning to use compression with parallel HDF5, ensure that calls to H5Dwrite() occur in collective mode. In other words, all MPI ranks (in the relevant communicator) call H5Dwrite() and pass a dataset transfer property list with the MPI-IO collective option property set to #H5FD_MPIO_COLLECTIVE_IO.\n Note that data transformations are currently \Bold{not} supported when writing to datasets in parallel and with compression enabled."
 ALIASES += sa_metadata_ops="\sa \li H5Pget_all_coll_metadata_ops() \li H5Pget_coll_metadata_write() \li H5Pset_all_coll_metadata_ops() \li H5Pset_coll_metadata_write() \li \ref maybe_metadata_reads"
 
+################################################################################
+# Specifications
+################################################################################
+
+ALIASES += ref_spec_fileformat="\ref FMT3"
+ALIASES += ref_spec_fileformat_btrees_v1="\ref subsubsec_fmt3_infra_btrees_v1"
+
 ################################################################################
 # References
 ################################################################################

diff --git a/doxygen/dox/HDF5CompressionTroubleshooting.dox b/doxygen/dox/HDF5CompressionTroubleshooting.dox
diff --git a/doxygen/dox/LearnBasics3.dox b/doxygen/dox/LearnBasics3.dox
@@ -107,7 +107,7 @@ which keeps track of the chunks associated with a dataset:
 
 
 \subsubsection susubsecLBDsetLayoutChunkWhy Why Chunking ?
-Chunking is required for enabling compression and other filters, as well as for creating extendible
+\ref hdf5_chunking is required for enabling compression and other filters, as well as for creating extendible
 or unlimited dimension datasets.
 
 It is also commonly used when subsetting very large datasets. Using the chunking layout can
@@ -149,6 +149,8 @@ It is a good idea to:
 \li Test the data with different chunk sizes to determine the optimal chunk size to use.
 \li Consider the chunk size in terms of the most common access patterns that will be used once the dataset has been created.
 
+@see hdf5_chunk_issues
+
 \subsection subsecLBDsetLayoutCom Compact
 A compact dataset is one in which the raw data is stored in the object header of the dataset.
 This layout is for very small datasets that can easily fit in the object header.

diff --git a/doxygen/dox/RelVersion.dox b/doxygen/dox/RelVersion.dox
@@ -260,4 +260,5 @@ Please note that this libtool version number for interface
 compatibility is unrelated to the HDF5 release version for a given
 release.
 
+@see BRANCHEXPL
 */
diff --git a/doxygen/dox/Specifications.dox b/doxygen/dox/Specifications.dox
@@ -1,20 +1,20 @@
 /** \page SPEC Specifications
 
-\section DDL
+\section sec_spec_ddl DDL
 
 \li \ref DDLBNF110
 \li \ref DDLBNF112
 \li \ref DDLBNF114
 \li \ref DDLBNF200
 
-\section File Format
+\section sec_spec_ff File Format
 
 \li \ref FMT1
 \li \ref FMT11
 \li \ref FMT2
 \li \ref FMT3
 
-\section Other
+\section sec_spec_other Other
 
 \li \ref IMG
 \li \ref TBLSPEC

diff --git a/doxygen/dox/TechnicalNotes.dox b/doxygen/dox/TechnicalNotes.dox
@@ -5,6 +5,7 @@
 \li \ref FMTDISC
 \li \ref BRANCHEXPL
 \li \ref CODECONV
+\li \ref CompTS
 \li \ref sec_file_image
 \li \ref subsubsec_dataset_transfer_filter
 \li \ref FileLock

diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
@@ -47,6 +47,8 @@ New Features
 
     Configuration:
     -------------
+    - The documentation in the source folder, doc, has been converted to doxygen files.
+
     - Added configuration option for API concurrency support:
 
           CMake:      HDF5_ENABLE_CONCURRENCY (ON/OFF) (Default: OFF)

diff --git a/src/H5Gmodule.h b/src/H5Gmodule.h
@@ -342,7 +342,7 @@
  * }
  * \endcode
  *
- * h5dump is described on the “HDF5 Tools” page of the \ref RM.
+ * \ref sec_cltools_h5dump is described on the \ref sec_cltools page of the \ref UG.
  *
  * The HDF5 DDL grammar is described in the @ref DDLBNF200.
  *

diff --git a/src/H5Zmodule.h b/src/H5Zmodule.h
@@ -100,6 +100,7 @@
  *
  * Filter identifiers for the filters distributed with the HDF5
  * Library are as follows:
+ * [PreDefFilters]
  * <table>
  *   <tr><td>#H5Z_FILTER_DEFLATE</td><td>The gzip compression, or
  *           deflation, filter</td></tr>
@@ -114,6 +115,7 @@
  *   <tr><td>#H5Z_FILTER_FLETCHER32</td><td>The Fletcher32 checksum,
  *           or error checking, filter</td></tr>
  * </table>
+ * [PreDefFilters]
  * Custom filters that have been registered with the library will have
  * additional unique identifiers.
  *

diff --git a/src/H5module.h b/src/H5module.h
@@ -1141,7 +1141,7 @@
  * </tr>
  * </table>
  *
- * HDF5 requires the use of chunking when defining extendable datasets. Chunking makes it
+ * HDF5 requires the use of chunking when defining extendable datasets. \ref hdf5_chunking makes it
  * possible to extend datasets efficiently without having to reorganize contiguous storage
  * excessively.
  *