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author | Allen Byrne <50328838+byrnHDF@users.noreply.github.com> | 2022-03-30 17:34:48 (GMT) |
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committer | GitHub <noreply@github.com> | 2022-03-30 17:34:48 (GMT) |
commit | fac4cd9e667e3ec6e62e7975fbdb53ff0d70cdc6 (patch) | |
tree | 73d047b9cf257c85a708eb813c12f3071ed6d67a /doxygen/dox | |
parent | d4f151fac40724b0425e697b1c3613b5d86cfa7b (diff) | |
download | hdf5-fac4cd9e667e3ec6e62e7975fbdb53ff0d70cdc6.zip hdf5-fac4cd9e667e3ec6e62e7975fbdb53ff0d70cdc6.tar.gz hdf5-fac4cd9e667e3ec6e62e7975fbdb53ff0d70cdc6.tar.bz2 |
1.10 Merge doxygen changes from develop (#1543)
* Merge doxygen changes from develop
* Remove 1.12 section
* Minor comment cleanup
Diffstat (limited to 'doxygen/dox')
-rw-r--r-- | doxygen/dox/About.dox | 118 | ||||
-rw-r--r-- | doxygen/dox/FTS.dox | 8 | ||||
-rw-r--r-- | doxygen/dox/Glossary.dox | 565 | ||||
-rw-r--r-- | doxygen/dox/H5AC_cache_config_t.dox | 6 | ||||
-rw-r--r-- | doxygen/dox/OtherSpecs.dox | 11 | ||||
-rw-r--r-- | doxygen/dox/Overview.dox | 38 | ||||
-rw-r--r-- | doxygen/dox/Specifications.dox | 38 | ||||
-rw-r--r-- | doxygen/dox/TechnicalNotes.dox | 28 | ||||
-rw-r--r-- | doxygen/dox/api-compat-macros.dox | 202 |
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> |