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-rw-r--r--doxygen/dox/About.dox118
-rw-r--r--doxygen/dox/FTS.dox8
-rw-r--r--doxygen/dox/Glossary.dox565
-rw-r--r--doxygen/dox/H5AC_cache_config_t.dox6
-rw-r--r--doxygen/dox/OtherSpecs.dox11
-rw-r--r--doxygen/dox/Overview.dox38
-rw-r--r--doxygen/dox/Specifications.dox38
-rw-r--r--doxygen/dox/TechnicalNotes.dox28
-rw-r--r--doxygen/dox/api-compat-macros.dox202
9 files changed, 778 insertions, 236 deletions
diff --git a/doxygen/dox/About.dox b/doxygen/dox/About.dox
index 32930a8..a8b31d7 100644
--- a/doxygen/dox/About.dox
+++ b/doxygen/dox/About.dox
@@ -12,12 +12,116 @@ of <em>documentation done right</em>.
\section about_documentation Documentation about Documentation
-\li \todo Describe how to add a reference or a new RFC
-\li \todo Describe how to add an example
-\li \todo Describe how to include plain HTML
-\li \todo Describe how to add an API macro
-\li \todo Describe the custom commands
-\li \todo Describe the S3 bucket layout and update routine
-\li \todo Link the RM template
+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!
*/ \ No newline at end of file
diff --git a/doxygen/dox/FTS.dox b/doxygen/dox/FTS.dox
new file mode 100644
index 0000000..9dae7c1
--- /dev/null
+++ b/doxygen/dox/FTS.dox
@@ -0,0 +1,8 @@
+/** \page FTS Full-Text Search
+
+\htmlonly
+<script async src="https://cse.google.com/cse.js?cx=75c754173f9b90804"></script>
+<div class="gcse-search"></div>
+\endhtmlonly
+
+*/ \ No newline at end of file
diff --git a/doxygen/dox/Glossary.dox b/doxygen/dox/Glossary.dox
new file mode 100644
index 0000000..9ccd27d
--- /dev/null
+++ b/doxygen/dox/Glossary.dox
@@ -0,0 +1,565 @@
+/** \page GLS Glossary
+
+\section GLS_A A
+
+<DL>
+ <DT>Array datatype</DT>
+ <DD>A family of HDF5 datatypes whose elements are arrays of a fixed rank (≤
+ 32) and fixed finite extent. All array elements must be of the same HDF5
+ datatype.</DD>
+</DL>
+
+<DL>
+ <DT>Array variable</DT>
+ <DD><P>A variable that can store (logically) dense, rectilinear, multidimensional
+ arrays of elements of a given HDF5 datatype.</P>
+ <P>The combination of array rank (dimensionality) and extent is called an
+ array variable's shape. This includes the degenerate array shapes of a
+ singleton (scalar) and the empty array (null).</P>
+ <P>The array element datatype is sometimes referred to as the array
+ variable's type, which is not entirely accurate because the array variable's
+ type is 'array of element type' rather than 'element type'.</P>
+ <P>In HDF5, there are two kinds of array variables, attributes and datasets,
+ and the distinction is functional (i.e., how they can be used) rather than
+ conceptual. Attributes are commonly used for descriptive "light-weight"
+ HDF5 object metadata while datasets are HDF5 objects used to store
+ "heavy-weight" problem-sized data.</P>
+ </DD>
+</DL>
+
+<DL>
+ <DT>Attribute</DT>
+ <DD><P>A named array variable that is associated with an HDF5 object, its
+ owner or attributee, and used to represent application domain-specific
+ metadata of the object. Intuitively, the set of an object's attributes can
+ be thought of as its key-value pair collection. Attribute names (keys) can
+ be arbitrary Unicode strings, but must be unique per object, i.e., an
+ object can have at most one attribute with a given name.</P>
+ <P>A scalar attribute is an attribute backed by a singleton array
+ variable. A null attribute is attribute backed by an empty array
+ variable.</P>
+</DD>
+</DL>
+
+\section GLS_B B
+
+<DL>
+ <DT>Bitfield datatype</DT>
+ <DD>A family of HDF5 datatypes whose elements are fixed-width bit fields.</DD>
+</DL>
+
+\section GLS_C C
+
+<DL>
+ <DT>Chunked layout</DT>
+ <DD>
+ <P>A dataset storage layout where the dataset elements are partitioned into
+ fixed-size multidimensional chunks or tiles. Chunked layout is mandatory
+ for datasets with one or more dimensions of indefinite (infinite) extent
+ or where compression or other filters are applied to the dataset elements.</P>
+ <P>Chunked layout may improve I/O performance for certain access patterns.</P>
+</DD>
+</DL>
+
+<DL>
+ <DT>Committed datatype</DT>
+ <DD>An immutable kind of HDF5 object that is used to store an HDF5 datatype
+ definition, which can be referenced by multiple array variables. When linked
+ to an HDF5 group, a committed datatype can be located by an HDF5 path name,
+ and is sometimes called a named datatype.</DD>
+</DL>
+
+<DL>
+ <DT>Compact layout</DT>
+ <DD></DD>
+</DL>
+
+<DL>
+ <DT>Compound datatype</DT>
+ <DD>
+ <P>A family of HDF5 datatypes whose elements are records with named fields
+ of other HDF5 datatypes. Currently, on ASCII field names are supported.</P>
+ <P>Similar to a <CODE>struct</CODE> in C or a <CODE>COMMON</CODE> block in
+ Fortran.</P>
+</DD>
+</DL>
+
+<DL>
+ <DT>Contiguous layout</DT>
+ <DD>A dataset storage layout where the dataset elements are physically stored
+ in an HDF5 file as a contiguous block of bytes.</DD>
+</DL>
+
+\section GLS_D D
+
+<DL>
+ <DT>Dataset</DT>
+ <DD>
+ <P>A kind of HDF5 object, a linked array variable. which can be located in
+ an HDF5 file through a path name. Datasets are commonly used to store
+ "heavy-weight" problem-sized data.</P>
+ <P>The HDF5 library offers a lot of features aimed at optimized dataset
+ access and storage, including compression and partial I/O.</P>
+</DD>
+</DL>
+
+<DL>
+ <DT>Dataspace</DT>
+ <DD>The shape of an array variable. With the exception of degenerate cases
+ (empty set, singleton), this is a rectilinear lattice or grid of a certain
+ rank (dimensionality) and extent.</DD>
+</DL>
+
+<DL>
+ <DT>Datatype</DT>
+ <DD>
+ <P>An HDF5 datatype consists of an abstract data type (a set of elements)
+ and a bit-level representation of these elements in storage such as an HDF5
+ file or memory.</P>
+ <P>The HDF5 library comes with a large set of predefined datatypes and
+ offers mechanisms for creating user-defined datatypes.</P>
+ <P>The ten major families or classes of HDF5 datatypes are:</P>
+ <UL>
+ <LI>Integer datatypes</LI>
+ <LI>Floating-point number datatypes</LI>
+ <LI>String datatypes</LI>
+ <LI>Bitfield datatypes</LI>
+ <LI>Opaque datatypes</LI>
+ <LI>Compound datatypes</LI>
+ <LI>Reference datatypes</LI>
+ <LI>Enumerated datatypes</LI>
+ <LI>Variable-length sequence datatypes</LI>
+ <LI>Array datatypes</LI>
+ </UL>
+</DD>
+</DL>
+
+\section GLS_E E
+
+<DL>
+ <DT>Enumeration datatype</DT>
+ <DD>A family of HDF5 datatypes whose elements represent named integer values
+ called members or enumerators. Currently, only ASCII names are supported.</DD>
+</DL>
+
+<DL>
+ <DT>External layout</DT>
+ <DD>A form of contiguous layout where a dataset's elements are physically
+ stored in unformatted binary files outside the HDF5 file.</DD>
+</DL>
+
+<DL>
+ <DT>External link</DT>
+ <DD>An HDF5 link whose destination is specified as a pair of an HDF5 file name
+and an HDF5 path name in that file.</DD>
+</DL>
+
+\section GLS_F F
+
+<DL>
+ <DT>Field</DT>
+ <DD>See compound datatype.</DD>
+</DL>
+
+<DL>
+ <DT>File</DT>
+ <DD>
+ <OL>
+ <LI>A byte stream (in a storage context such as a file system or in
+ memory) formatted according to the HDF5 File Format Specification.</LI>
+ <LI>A (logical) container for HDF5 objects.</LI>
+ </OL>
+ </DD>
+</DL>
+
+<DL>
+ <DT>File format</DT>
+ <DD></DD>
+</DL>
+
+<DL>
+ <DT>Fill value</DT>
+ <DD></DD>
+</DL>
+
+<DL>
+ <DT>Filter</DT>
+ <DD></DD>
+</DL>
+
+\section GLS_G G
+
+<DL>
+ <DT>Group</DT>
+ <DD>
+ <P>A kind of HDF5 object that stores a collection of HDF5 links. Each HDF5
+ file contains at least one group, it's root group.</P>
+ <P>Among the destinations of an HDF5 group's links may be other HDF5 groups
+ (including the group itself!). This ability is sometimes referred to as the
+ closure property of groups. It is the basis for creating hierarchical or
+ more general graph-like structures.</P>
+</DD>
+</DL>
+
+\section GLS_H H
+
+<DL>
+ <DT>Hard link</DT>
+ <DD>An HDF5 link whose destination is specified (internally) as the address of
+ an HDF5 object in the same HDF5 file.</DD>
+</DL>
+
+<DL>
+ <DT>Hierarchy</DT>
+ <DD>See group.</DD>
+</DL>
+
+<DL>
+ <DT>Hyperslab</DT>
+ <DD>
+ <P>A regular multidimensional pattern described by four vectors whose length
+ equals the rank of the pattern.</P>
+ <OL>
+ <LI><CODE>start</CODE> - the offset where the first block of the hyperslab begins</LI>
+ <LI><CODE>stride</CODE> - the offset between pattern blocks</LI>
+ <LI><CODE>count</CODE> - the number of blocks</LI>
+ <LI><CODE>block</CODE> - the extent of an individual pattern block</LI>
+ </OL>
+ <P>For example, the black squares on a (two-dimensional) chessboard with
+ origin at <CODE>(0,0)</CODE> can be represented as the union of two
+ hyperslabs representing the even <CODE>(0,2,4,6)</CODE> and
+ odd <CODE>(1,3,5,7)</CODE> rows, respectively.</P>
+ <IMG SRC="https://upload.wikimedia.org/wikipedia/commons/thumb/d/d7/Chessboard480.svg/176px-Chessboard480.svg.png"/>
+ <P>The hyperslab parameters for the even rows are: <CODE>start (0,0)</CODE>,
+ <CODE>stride (2,2)</CODE>, <CODE>count (4,4)</CODE>, <CODE>block
+ (1,1)</CODE>. Likewise the parameters for the odd rows are: <CODE>start
+ (1,1)</CODE>, <CODE>stride (2,2)</CODE>, <CODE>count
+ (4,4)</CODE>, <CODE>block (1,1)</CODE>.</P>
+</DD>
+</DL>
+
+\section GLS_I I
+
+<DL>
+ <DT>Identifier</DT>
+ <DD>An opaque, transient handle used by the HDF5 library to manipulate
+ in-memory representations of HDF5 items.</DD>
+</DL>
+
+\section GLS_L L
+
+<DL>
+ <DT>Library</DT>
+ <DD></DD>
+</DL>
+
+<DL>
+ <DT>Link</DT>
+ <DD>
+ <P>A named, uni-directional association between a source and a
+ destination. In HDF5, the source is always the HDF5 group that hosts the
+ link in its link collection.</P>
+ <P>There are several ways to specify a link's destination:</P>
+ <UL>
+ <LI>The address of an HDF5 object in the same HDF5 file; so-called hard
+ link.</LI>
+ <LI>A path name in the same or a different file; so-called soft or
+ external link.</LI>
+ <LI>User-defined</LI>
+ </UL>
+ <P>A link name can be any Unicode string that does not contain slashes
+ (<CODE>"/"</CODE>) or consists of a single dot character
+ (<CODE>"."</CODE>). A link name must be unique in a group's link
+ collection.</P>
+ </DD>
+</DL>
+
+\section GLS_M M
+
+<DL>
+ <DT>Metadata</DT>
+ <DD>Data that in a given context has a descriptive or documentation function
+ for other data. Typically, the metadata is small compared to the data it
+ describes.</DD>
+</DL>
+
+<DL>
+ <DT>Member</DT>
+ <DD>
+ <P>A link destination is sometimes referred to as a member of the link's
+ source (group). This way of speaking invites confusion: A destination (e.g.,
+ object) can be the destination of multiple links in the same (!) or
+ different groups. It would then be a "member" of a given group with
+ multiplicity greater than one and be a member of multiple groups.</P>
+ <P> It is the link that is a member of the group's link collection and not
+ the link destination.</P>
+ </DD>
+</DL>
+
+\section GLS_N N
+
+<DL>
+ <DT>Name</DT>
+ <DD>
+ <P>A Unicode string that depending on the item it names might be subject to
+ certain character restrictions, such as ASCII-encoded only. In HDF5, the
+ user might encounter the following names:</P>
+ <UL>
+ <LI>A link name</LI>
+ <LI>A path name</LI>
+ <LI>An attribute name</LI>
+ <LI>A field name (compound datatypes)</LI>
+ <LI>A constant name (enumeration datatypes)</LI>
+ <LI>A tag name (opaque datatypes)</LI>
+ <LI>A file name</LI>
+ </UL>
+ </DD>
+</DL>
+
+
+<DL>
+ <DT>Named datatype</DT>
+ <DD>See committed datatype.</DD>
+</DL>
+
+<DL>
+ <DT>Null dataspace</DT>
+ <DD>A shape which represents the empty set. Array variables with this shape
+ cannot store any values.</DD>
+</DL>
+
+\section GLS_O O
+
+<DL>
+ <DT>Object</DT>
+ <DD>An HDF5 group, dataset or named datatype; an HDF5 item that can be linked
+ to zero or more groups and decorated with zero or more HDF5 attributes.</DD>
+</DL>
+
+<DL>
+ <DT>Object reference</DT>
+ <DD>
+ <OL>
+ <LI>A datatype for representing references to objects in a file.</LI>
+ <LI>A value of the object reference datatype.</LI>
+ </OL>
+ </DD>
+</DL>
+
+<DL>
+ <DT>Opaque datatype</DT>
+ <DD>A family of HDF5 datatypes whose elements are byte sequences of a given
+ fixed length. An opaque datatype can be tagged with a sequence of up to 256
+ ASCII characters, e.g., MIME code.</DD>
+</DL>
+
+\section GLS_P P
+
+<DL>
+ <DT>Path name</DT>
+ <DD>A Unicode string that is the concatenation of link names separated by
+ slashes (<CODE>'/'</CODE>). In HDF5, path names are used to locate and refer
+ to HDF5 objects.</DD>
+</DL>
+
+<DL>
+ <DT>Plugin</DT>
+ <DD>An HDF5 library feature or capability that can be added dynamically at
+ application run time rather than library compilation time. Plugins are
+ usually implemented as shared libraries, and their discovery and loading
+ behavior can be controlled programmatically or through environment
+ variables.
+ </DD>
+</DL>
+
+<DL>
+ <DT>Point selection</DT>
+ <DD>A dataspace selection that consists of a set of points (coordinates) in
+ the same dataspace.</DD>
+</DL>
+
+<DL>
+ <DT>Property list</DT>
+ <DD>
+ <P>An HDF5 API construct, a means of customizing the behavior of the HDF5
+ library when creating, accessing or modifying HDF5 items.</P>
+ <P>While the default property settings are sufficient in many cases, certain
+ HDF5 features, such as compression, can be reasonably controlled only by the
+ user who has to provide the desired settings via property lists.</P>
+</DD>
+</DL>
+
+\section GLS_R R
+
+<DL>
+ <DT>Rank</DT>
+ <DD>The number of dimensions of a non-null dataspace.</DD>
+</DL>
+
+<DL>
+ <DT>Reference</DT>
+ <DD>
+ <OL>
+ <LI>An HDF5 object reference</LI>
+ <LI>An HDF5 dataset region reference</LI>
+ </OL>
+ </DD>
+</DL>
+
+<DL>
+ <DT>Reference datatype</DT>
+ <DD>
+ <OL>
+ <LI>An HDF5 datatype whose elements represent references to HDF5
+ objects.</LI>
+ <LI>An HDF5 datatype whose elements represent references to regions of an
+ HDF5 dataset.</LI>
+ </OL>
+ </DD>
+</DL>
+
+<DL>
+ <DT>Region reference</DT>
+ <DD>See dataset region reference.</DD>
+</DL>
+
+<DL>
+ <DT>Root group</DT>
+ <DD>
+ <P>An HDF5 group that is present in all HDF5 files and that acts as the
+ entry or base point for all other data stored in an HDF5 file.</P>
+ <P>The root group is "the mother of all objects" in an HDF5 file in the
+ sense that all objects (and their attributes) can be discovered,
+ beginning at the root group, by combinations of the following
+ operations:</P>
+ <UL>
+ <LI>Link traversal</LI>
+ <LI>De-referencing of object references</LI>
+ </UL>
+ <P>This discovery is portable and robust with respect to file-internal
+ storage reorganization.</P>
+</DD>
+</DL>
+
+\section GLS_S S
+
+<DL>
+ <DT>Scalar dataspace</DT>
+ <DD>A kind of HDF5 dataspace that has the shape of a singleton, i.e., a set
+ containing a single element. Array variables with this shape store exactly one
+ element.</DD>
+</DL>
+
+<DL>
+ <DT>Selection</DT>
+ <DD>
+ <OL>
+ <LI>A subset of points of an HDF5 dataspace. The subset might be a point
+ selection or a combination (union, intersection, etc.) of hyperslabs.</LI>
+ <LI>A subset of dataset elements associated with a dataspace selection as
+ described under 1.</LI>
+ </OL>
+ </DD>
+</DL>
+
+<DL>
+ <DT>Serialization</DT>
+ <DD>
+ <OL>
+ <LI>The flattening of an N-dimensional array into a 1-dimensional
+ array.</LI>
+ <LI>The encoding of a complex data item as a linear byte stream.</LI>
+ </OL>
+ </DD>
+</DL>
+
+<DL>
+ <DT>Soft link</DT>
+ <DD>A kind of HDF5 link in which the link destination is specified as an HDF5
+ path name. The path name may or may not refer to an actual object.</DD>
+</DL>
+
+<DL>
+ <DT>Storage layout</DT>
+ <DD>The storage arrangement for dataset elements, links in a group's link
+ collection, or attributes in an object's attribute collection.</DD>
+</DL>
+
+<DL>
+ <DT>String datatype</DT>
+ <DD></DD>
+</DL>
+
+<DL>
+ <DT>Super block</DT>
+ <DD>An HDF5 file format primitive; a block of data which contains information
+ required to access HDF5 files in a portable manner on multiple platforms. The
+ super block contains information such as version numbers, the size of offsets
+ and lengths, and the location of the root group.</DD>
+</DL>
+
+<DL>
+ <DT>SWMR</DT>
+ <DD>Single Writer Multiple Reader, a file access mode in which a single
+ process is permitted to write data to an HDF5 file while other processes are
+ permitted to read data from the same file without the need of inter-process
+ communication or synchronization.</DD>
+</DL>
+
+<DL>
+ <DT>Symbolic link</DT>
+ <DD>An external link or a soft link.</DD>
+</DL>
+
+\section GLS_U U
+
+<DL>
+ <DT>User block</DT>
+ <DD>An HDF5 file format primitive that allows one to set aside a fixed-size
+ (at least 512 bytes or any power of 2 thereafter) contiguous range of bytes at
+ the beginning of an HDF5 file for application purposes which will be
+ skipped/ignored by the HDF5 library.</DD>
+</DL>
+
+<DL>
+ <DT>UTF-8</DT>
+ <DD>
+ <P>A variable-length (1-4 bytes per code point) encoding of the Unicode set
+ of code points. This is the encoding supported by HDF5 to represent Unicode
+ strings.</P>
+ <P>The ASCII encoding is a proper subset of UTF-8.</P>
+</DD>
+</DL>
+
+\section GLS_V V
+
+<DL>
+ <DT>Variable-length (sequence) datatype</DT>
+ <DD>A family of HDF5 datatypes whose elements are variable-length sequences of
+ a given datatype.</DD>
+</DL>
+
+<DL>
+ <DT>Virtual Dataset (VDS)</DT>
+ <DD>An HDF5 dataset with virtual storage layout. A dataset whose elements are
+ partially or entirely stored physically in other datasets.</DD>
+</DL>
+
+<DL>
+ <DT>Virtual File Driver (VFD)</DT>
+ <DD></DD>
+</DL>
+
+
+<DL>
+ <DT>Virtual layout</DT>
+ <DD></DD>
+</DL>
+
+
+<DL>
+ <DT>Virtual Object Layer (VOL)</DT>
+ <DD></DD>
+</DL>
+
+*/
diff --git a/doxygen/dox/H5AC_cache_config_t.dox b/doxygen/dox/H5AC_cache_config_t.dox
index 9b9862b..3faecd5 100644
--- a/doxygen/dox/H5AC_cache_config_t.dox
+++ b/doxygen/dox/H5AC_cache_config_t.dox
@@ -26,7 +26,7 @@
*
* \Emph{*** DEPRECATED ***} Use \Code{H5Fstart/stop} logging functions instead
*
- * The trace file is a debuging feature that allow the capture of
+ * The trace file is a debugging feature that allow the capture of
* top level metadata cache requests for purposes of debugging and/or
* optimization. This field should normally be set to \c FALSE, as
* trace file collection imposes considerable overhead.
@@ -82,7 +82,7 @@
* H5C_incr__off ) && ( decr_mode == H5C_decr__off )}). There
* is no logical reason why this should be so, but it simplifies
* implementation and testing, and I can't think of any reason
- * why it would be desireable. If you can think of one, I'll
+ * why it would be desirable. If you can think of one, I'll
* revisit the issue. (JM)
* \endparblock
*
@@ -383,7 +383,7 @@
* to disk.\n
* When the sync point is reached (or when there is a user generated
* flush), process zero flushes sufficient entries to bring it into
- * complience with its min clean size (or flushes all dirty entries in
+ * compliance with its min clean size (or flushes all dirty entries in
* the case of a user generated flush), broad casts the list of
* entries just cleaned to all the other processes, and then exits
* the sync point.\n
diff --git a/doxygen/dox/OtherSpecs.dox b/doxygen/dox/OtherSpecs.dox
deleted file mode 100644
index e53f26e..0000000
--- a/doxygen/dox/OtherSpecs.dox
+++ /dev/null
@@ -1,11 +0,0 @@
-/** \page IMG HDF5 Image and Palette Specification Version 1.2
-
-\htmlinclude ImageSpec.html
-
-*/
-
-/** \page TBL HDF5 Table Specification Version 1.0
-
-\htmlinclude TableSpec.html
-
-*/
diff --git a/doxygen/dox/Overview.dox b/doxygen/dox/Overview.dox
index 754722e..040769c 100644
--- a/doxygen/dox/Overview.dox
+++ b/doxygen/dox/Overview.dox
@@ -1,14 +1,12 @@
/** \mainpage notitle
-This is the documentation set for HDF5. You can
-<a href="hdf5-doc.tgz">download</a> it as a tgz archive for offline reading.
-
-This is the documention set for HDF5 in terms of specifications and software
-developed and maintained by <a href="https://www.hdfgroup.org/">The HDF
-Group</a>. It is impractical to document the entire HDF5 ecosystem in one place,
-and you should also consult the documentation sets of the many outstanding
-community projects.
+This is the documentation set for HDF5.
+It includes specifications and documentation
+of software and tools developed and maintained by
+<a href="https://www.hdfgroup.org/">The HDF Group</a>. It is impractical to document
+the entire HDF5 ecosystem in one place, and you should also consult the documentation
+sets of the many outstanding community projects.
For a first contact with HDF5, the best place is to have a look at the \link
GettingStarted getting started \endlink page that shows you how to write and
@@ -19,12 +17,28 @@ technical documentation consists to varying degrees of information related to
<em>tasks</em>, <em>concepts</em>, or <em>reference</em> material. As its title
suggests, the \link RM Reference Manual \endlink is 100% reference material,
while the \link Cookbook \endlink is focused on tasks. The different guide-type
-documents cover a mix of tasks, concepts, and reference, to help a certain
+documents cover a mix of tasks, concepts, and reference, to help a specific
<em>audience</em> succeed.
-Finally, do not miss the search engine (top right-hand corner)! If you are
-looking for a specific function, it'll take you there directly. If unsure, it'll
-give you an idea of what's on offer and a few promising leads.
+\par Versions
+ Version-specific documentation (see the version in the title area) can be found
+ here:
+ - HDF5 <code>develop</code> branch (this site)
+ - <a href="https://docs.hdfgroup.org/hdf5/v1_12/index.html">HDF5 1.12.x</a>
+ - <a href="https://docs.hdfgroup.org/hdf5/v1_10/index.html">HDF5 1.10.x</a>
+ - <a href="https://docs.hdfgroup.org/hdf5/v1_8/index.html">HDF5 1.8.x</a>
+
+\par Search
+ If you are looking for a specific function, constant, type, etc., use the
+ search box in the top right-hand corner!\n Otherwise, check out the
+ \link FTS full-text search\endlink.
+
+\par Offline reading
+ You can <a href="hdf5-doc.tgz">download</a> it as a tgz archive for offline reading.
+
+\par History
+ A snapshot (~April 2017) of the pre-Doxygen HDF5 documentation can be found
+ <a href="https://docs.hdfgroup.org/archive/support/HDF5/doc/index.html">here</a>.
\par ToDo List
There is plenty of <a href="./todo.html">unfinished business</a>.
diff --git a/doxygen/dox/Specifications.dox b/doxygen/dox/Specifications.dox
index bd7e849..f6fee78 100644
--- a/doxygen/dox/Specifications.dox
+++ b/doxygen/dox/Specifications.dox
@@ -18,4 +18,40 @@
\li <a href="https://support.hdfgroup.org/HDF5/doc/HL/H5DS_Spec.pdf">
HDF5 Dimension Scale Specification</a>
-*/ \ No newline at end of file
+*/
+
+/** \page FMT3 HDF5 File Format Specification Version 3.0
+
+\htmlinclude H5.format.html
+
+*/
+
+/** \page FMT2 HDF5 File Format Specification Version 2.0
+
+\htmlinclude H5.format.2.0.html
+
+*/
+
+/** \page FMT11 HDF5 File Format Specification Version 1.1
+
+\htmlinclude H5.format.1.1.html
+
+*/
+
+/** \page FMT1 HDF5 File Format Specification Version 1.0
+
+\htmlinclude H5.format.1.0.html
+
+*/
+
+/** \page IMG HDF5 Image and Palette Specification Version 1.2
+
+\htmlinclude ImageSpec.html
+
+*/
+
+/** \page TBL HDF5 Table Specification Version 1.0
+
+\htmlinclude TableSpec.html
+
+*/
diff --git a/doxygen/dox/TechnicalNotes.dox b/doxygen/dox/TechnicalNotes.dox
index 2bda175..9bd2802 100644
--- a/doxygen/dox/TechnicalNotes.dox
+++ b/doxygen/dox/TechnicalNotes.dox
@@ -1,6 +1,10 @@
/** \page TN Technical Notes
\li \link api-compat-macros API Compatibility Macros \endlink
+\li \ref APPDBG "Debugging HDF5 Applications"
+\li \ref FMTDISC "File Format Walkthrough"
+\li \ref FILTER "Filters"
+\li \ref IOFLOW "HDF5 Raw I/O Flow Notes"
\li \ref TNMDC "Metadata Caching in HDF5"
\li \ref MT "Thread Safe library"
\li \ref VFL "Virtual File Layer"
@@ -13,8 +17,32 @@
*/
+/** \page IOFLOW HDF5 Raw I/O Flow Notes
+
+\htmlinclude IOFlow.html
+
+*/
+
/** \page VFL HDF5 Virtual File Layer
\htmlinclude VFL.html
*/
+
+/** \page FMTDISC HDF5 File Format Discussion
+
+\htmlinclude FileFormat.html
+
+*/
+
+/** \page FILTER HDF5 Filters
+
+\htmlinclude Filters.html
+
+*/
+
+/** \page APPDBG Debugging HDF5 Applications
+
+\htmlinclude DebuggingHDF5Applications.html
+
+*/ \ No newline at end of file
diff --git a/doxygen/dox/api-compat-macros.dox b/doxygen/dox/api-compat-macros.dox
index 4a1578d..6b506a1 100644
--- a/doxygen/dox/api-compat-macros.dox
+++ b/doxygen/dox/api-compat-macros.dox
@@ -300,208 +300,6 @@
-DH5Lget_info_vers=1 application.c
\endcode
- \subsubsection fun-options-112 Function Mapping Options in Releases 1.12.x
- <table>
- <tr>
- <th style="text-align: left;">Macro <br/> (\Code{H5xxx})</th>
- <th>Default function used if no macro specified
- <ul><li>Function/struct mapping:\Code{H5xxx_vers=N}</li></ul>
- </th>
- <th>Function used if specifying 1.10
- <ul><li>Function/struct mapping: \Code{H5xxx_vers=1}</li></ul>
- </th>
- </tr>
- <tr>
- <td>H5Lget_info()</td>
- <td>H5Lget_info2()
- <ul>
- <li>Function mapping:\Code{H5Lget_info_vers=2}</li>
- <li>Struct mapping:\Code{H5L_info_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Lget_info1()
- <ul>
- <li>Function mapping \Code{H5Lget_info_vers=1}</li>
- <li>Struct mapping: \Code{H5L_info_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Lget_info_by_idx()</td>
- <td>H5Lget_info_by_idx2()
- <ul>
- <li>Function mapping: \Code{H5Lget_info_by_idx_vers=2}</li>
- <li>Struct mapping: \Code{H5L_info_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Lget_info_by_idx1()
- <ul>
- <li>Function mapping: \Code{H5Lget_info_by_idx_vers=1}</li>
- <li>Struct mapping: \Code{H5L_info_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Literate()</td>
- <td>H5Literate2()
- <ul>
- <li>Function mapping: \Code{H5Literate_vers=2}</li>
- <li>Struct mapping: \Code{H5L_iterate_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Literate1()
- <ul>
- <li>Function mapping: \Code{H5Literate_vers=1}</li>
- <li>Struct mapping: \Code{H5L_iterate_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Literate_by_name()</td>
- <td>H5Literate_by_name2()
- <ul>
- <li>Function mapping: \Code{H5Literate_by_name_vers=2}</li>
- <li>Struct mapping: \Code{H5L_iterate_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Literate_by_name1()
- <ul>
- <li>Function mapping: \Code{H5Literate_by_name_vers=1}</li>
- <li>Struct mapping: \Code{H5L_iterate_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Lvisit()</td>
- <td>H5Lvisit2()
- <ul>
- <li>Function mapping: \Code{H5Lvisit_vers=2}</li>
- <li>Struct mapping: \Code{H5L_iterate_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Lvisit1()
- <ul>
- <li>Function mapping: \Code{H5Lvisit_vers=1}</li>
- <li>Struct mapping: \Code{H5L_iterate_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Lvisit_by_name()</td>
- <td>H5Lvisit_by_name2()
- <ul>
- <li>Function mapping: \Code{H5Lvisit_by_name_vers=2}</li>
- <li>Struct mapping: \Code{H5L_iterate_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Lvisit_by_name1()
- <ul>
- <li>Function mapping: \Code{H5Lvisit_by_name_vers=1}</li>
- <li>Struct mapping: \Code{H5L_iterate_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Oget_info()</td>
- <td>H5Oget_info3()
- <ul>
- <li>Function mapping: \Code{H5Oget_info_vers=3}</li>
- <li>Struct mapping: \Code{H5O_info_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Oget_info1()
- <ul>
- <li>Function mapping: \Code{H5Oget_info_vers=1}</li>
- <li>Struct mapping: \Code{H5O_info_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Oget_info_by_idx()</td>
- <td>H5Oget_info_by_idx3()
- <ul><li>Function mapping: \Code{H5Oget_info_by_idx_vers=3}</li>
- <li>Struct mapping: \Code{H5O_info_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Oget_info_by_idx1()
- <ul>
- <li>Function mapping: \Code{H5Oget_info_by_idx_vers=1}</li>
- <li>Struct mapping: \Code{H5O_info_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Oget_info_by_name()</td>
- <td>H5Oget_info_by_name3()
- <ul>
- <li>Function mapping: \Code{H5O_get_info_by_name_vers=3}</li>
- <li>Struct mapping: \Code{H5O_info_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Oget_info_by_name1()
- <ul>
- <li>Function mapping: \Code{H5O_get_info_by_name_vers=1}</li>
- <li>Struct mapping: \Code{H5O_info_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Ovisit()</td>
- <td>H5Ovisit3()
- <ul>
- <li>Function mapping: \Code{H5Ovisit_vers=3}</li>
- <li>Struct mapping: \Code{H5O_iterate_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Ovisit1()
- <ul><li>Function mapping: \Code{H5Ovisit_vers=1}</li>
- <li>Struct mapping: \Code{H5O_iterate_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Ovisit_by_name()</td>
- <td>H5Ovisit_by_name3()
- <ul>
- <li>Function mapping: \Code{H5Ovisit_by_name_vers=3}</li>
- <li>Struct mapping: \Code{H5O_iterate_t_vers=2}</li>
- </ul>
- </td>
- <td>H5Ovisit_by_name1()
- <ul>
- <li>Function mapping: \Code{H5Ovisit_by_name_vers=1}</li>
- <li>Struct mapping: \Code{H5O_iterate_t_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Pencode()</td>
- <td>H5Pencode2()
- <ul>
- <li>Function mapping: \Code{H5Pencode_vers=2}</li>
- </ul>
- </td>
- <td>H5Pencode1()
- <ul>
- <li>Function mapping: \Code{H5Pencode_vers=1}</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td>H5Sencode()</td>
- <td>H5Sencode2()
- <ul>
- <li>Function mapping: \Code{H5Sencode_vers=2}</li>
- </ul>
- </td>
- <td>H5Sencode1()
- <ul>
- <li>Function mapping: \Code{H5Sencode_vers=1}</li>
- </ul>
- </td>
- </tr>
- </table>
-
\subsubsection fun-options-110 Function Mapping Options in Releases 1.10.x
<table>
<tr>
generated by cgit v0.12 at 2024-07-05 01:21:36 (GMT)