Correct doxygen GH pages folder for release (#4395)

* Correct wild link for HL

* Add md pattern

* Correct markdown image ref

* Correct new markdown issues

* Fix anchors

* fix typo

* Use EXCLUDE_PATTERNS

* Correct ref syntax

.github/workflows/release-files.yml

@@ -230,9 +230,9 @@ jobs:
               ls -l ${{ github.workspace }}
               ls ${{ runner.workspace }}
 
-      - name: branch-only-docs
+      - name: rel-branch-only-docs
         uses: peaceiris/actions-gh-pages@373f7f263a76c20808c831209c920827a82a2847 # v3.9.3
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ${{ github.workspace }}/${{ steps.get-file-base.outputs.FILE_BASE }}.doxygen
-          destination_dir: v1_14
+          destination_dir: v1_14_4

CONTRIBUTING.md

@@ -16,12 +16,12 @@ around 10 minutes.
 
 ## Table of Contents
 
-* [Workflow](#workflow)
-* [Acceptance criteria for a pull request](#criteria)
-* [Release Note](#releasenote)
-* [Check List](#checklist)
+* <a href="#workflow">Workflow</a>
+* <a href="#criteria">Acceptance criteria for a pull request</a>
+* <a href="#releasenote">Release Note</a>
+* <a href="#checklist">Check List</a>
 
-# Workflow <A NAME="workflow"></A>
+<h2 id="workflow">Workflow</h2>
 
 The process for contributing code to HDF5 is as follows:
 
@@ -41,7 +41,7 @@ Once a pull request is correctly formatted and passes **ALL** CI tests, it will
 community members who can approve pull requests. The HDF Group developers will work with you to ensure that the pull request satisfies the acceptance
 criteria described in the next section.
 
-# Acceptance criteria for a pull request <A NAME="criteria"></A>
+<h2 id="criteria">Acceptance criteria for a pull request</h2>
 
 We appreciate every contribution we receive, but we may not accept them all.  Those that we *do* satisfy the following criteria:
 
@@ -84,7 +84,7 @@ application developers and not system administrators. Users who may find the REL
 application developers, library developers, and system administrators.
 
 
-# Release Note <A NAME="releasenote"></A>
+<h2 id="releasenote">Release Note</h2>
 
 * **Entry Syntax**
 The release note entry syntax is shown below.
@@ -112,7 +112,7 @@ You might also consider the following as you describe the solution:
         * Is there a workaround – a way for users design their software so as not to encounter the issue? If so, what is the workaround?
         * For a performance fix, how has the performance improved? Links to published documentation would be good.
 
-# Checklist <A NAME="checklist"></A>
+<h2 id="checklist">Checklist</h2>
 
 Please make sure that you check the items applicable to your pull request:
 
@@ -122,10 +122,10 @@ Please make sure that you check the items applicable to your pull request:
   * [ ] If changes were done to Autotools build, were they added to CMake and vice versa?
   * [ ] Is the pull request applicable to any other branches? If yes, which ones? Please document it in the GitHub issue.
   * [ ] Is the new code sufficiently documented for future maintenance?
-  * [ ] Does the new feature require a change to an existing API? See "API Compatibility Macros" document (https://docs.hdfgroup.org/hdf5/v1_14/api-compat-macros.html)
+  * [ ] Does the new feature require a change to an existing API? See "API Compatibility Macros" document (https://docs.hdfgroup.org/hdf5/v1_14_4/api-compat-macros.html)
 * Documentation
   * [ ] Was the change described in the release_docs/RELEASE.txt file?
-  * [ ] Was the new function documented in the corresponding public header file using [Doxygen](https://hdfgroup.github.io/hdf5/v1_14/_r_m_t.html)?
+  * [ ] Was the new function documented in the corresponding public header file using [Doxygen](https://hdfgroup.github.io/hdf5/v1_14_4/_r_m_t.html)?
   * [ ] Was new functionality documented for the HDF5 community (the level of documentation depends on the feature; ask us what would be appropriate)
 * Testing
   * [ ] Does the pull request have tests?

README.md

@@ -21,11 +21,11 @@ DOCUMENTATION
 -------------
 This release is fully functional for the API described in the documentation.
 
-   https://docs.hdfgroup.org/hdf5/v1_14/_l_b_a_p_i.html
+   https://docs.hdfgroup.org/hdf5/v1_14_4/_l_b_a_p_i.html
 
 Full Documentation and Programming Resources for this release can be found at
 
-   https://docs.hdfgroup.org/hdf5/v1_14/index.html
+   https://docs.hdfgroup.org/hdf5/v1_14_4/index.html
 
 The latest doxygen documentation generated on changes to HDF5 1.14.x is available at:
 

doxygen/Doxyfile.in

@@ -688,6 +688,7 @@ FILE_PATTERNS  = H5*public.h H5*module.h H5*develop.h H5FD*.h \
                  HDF*.java \
                  *.F90 \
                  *.dox \
+                 *.md \
                  H5Cpp.h H5AbstractDs.h H5AtomType.h H5Attribute.h H5CommonFG.h H5CompType.h \
                  H5DataSet.h H5DataSpace.h H5DataType.h H5OcreatProp.h H5DaccProp.h H5DcreatProp.h \
                  H5DxferProp.h H5EnumType.h H5Exception.h H5FaccProp.h H5FcreatProp.h H5File.h \
@@ -708,8 +709,7 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = examples
-
+EXCLUDE                =
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
 # from the input.
@@ -734,6 +734,8 @@ EXCLUDE_PATTERNS      += */hl/fortran/test/*
 EXCLUDE_PATTERNS      += */hl/fortran/src/*.c
 EXCLUDE_PATTERNS      += */hl/fortran/src/*.h
 EXCLUDE_PATTERNS      += */HDF5Examples/FORTRAN/*
+EXCLUDE_PATTERNS      += */sanitizer/*
+
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the

doxygen/aliases

@@ -237,7 +237,7 @@ ALIASES += sa_metadata_ops="\sa \li H5Pget_all_coll_metadata_ops() \li H5Pget_co
 ALIASES += ref_cons_semantics="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/RFC%20PHDF5%20Consistency%20Semantics%20MC%20120328.docx.pdf\">Enabling a Strict Consistency Semantics Model in Parallel HDF5</a>"
 ALIASES += ref_file_image_ops="<a href=\"https://docs.hdfgroup.org/hdf5/rfc/HDF5FileImageOperations.pdf\">HDF5 File Image Operations</a>"
 ALIASES += ref_filter_pipe="<a href=\"https://portal.hdfgroup.org/display/HDF5/HDF5+Data+Flow+Pipeline+for+H5Dread\">Data Flow Pipeline for H5Dread()</a>"
-ALIASES += ref_group_impls="<a href=\"https://docs.hdfgroup.org/hdf5/v1_14/group___h5_g.html\">Group implementations in HDF5</a>"
+ALIASES += ref_group_impls="<a href=\"https://docs.hdfgroup.org/hdf5/v1_14_4/group___h5_g.html\">Group implementations in HDF5</a>"
 ALIASES += ref_h5lib_relver="<a href=\"https://docs.hdfgroup.org/archive/support/HDF5/doc/TechNotes/Version.html\">HDF5 Library Release Version Numbers</a>"
 ALIASES += ref_mdc_in_hdf5="<a href=\"https://portal.hdfgroup.org/display/HDF5/Metadata+Caching+in+HDF5\">Metadata Caching in HDF5</a>"
 ALIASES += ref_mdc_logging="<a href=\"https://portal.hdfgroup.org/display/HDF5/H5F_START_MDC_LOGGING\">Metadata Cache Logging</a>"

doxygen/dox/GettingStarted.dox

@@ -42,10 +42,10 @@ Parallel HDF5, and the HDF5-1.10 VDS and SWMR new features:
 <table>
 <tr>
 <td style="background-color:#F5F5F5">
-<a href="https://docs.hdfgroup.org/hdf5/develop/high_level.html">Using the High Level APIs</a>
+[Using the High Level API](../examples/menus/high_level_menu.md)
 </td>
 <td>
-\ref H5LT    \ref H5IM    \ref H5TB    \ref H5PT    \ref H5DS
+The high-level HDF5 library includes several sets of convenience and standard-use APIs to facilitate common HDF5 operations.
 </td>
 </tr>
 <tr>
@@ -72,7 +72,7 @@ HDF5-1.10 New Features
 </td>
 <td>
 \li <a href="https://portal.hdfgroup.org/display/HDF5/Introduction+to+the+Virtual+Dataset++-+VDS">Introduction to the Virtual Dataset - VDS</a>
-\li <a href="https://docs.hdfgroup.org/hdf5/v1_14/group___s_w_m_r.html">Introduction to Single-Writer/Multiple-Reader (SWMR)</a>
+\li <a href="https://docs.hdfgroup.org/hdf5/v1_14_4/group___s_w_m_r.html">Introduction to Single-Writer/Multiple-Reader (SWMR)</a>
 </td>
 </tr>
 <tr>

doxygen/dox/Overview.dox

@@ -24,7 +24,7 @@ documents cover a mix of tasks, concepts, and reference, to help a specific
      Version-specific documentation (see the version in the title area) can be found
      here:
      - <a href="https://hdfgroup.github.io/hdf5/develop/index.html">HDF5 <code>develop</code> branch</a>
-     - <a href="https://hdfgroup.github.io/hdf5/v1_14/index.html">HDF5 1.14.x (this site)</a>
+     - <a href="https://hdfgroup.github.io/hdf5/v1_14_4/index.html">HDF5 1.14.x (this site)</a>
      - <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>

doxygen/dox/ViewTools.dox

@@ -997,7 +997,7 @@ In other words, it is an array of four elements, in which each element is a 3 by
 
 This dataset is much more complex. Also note that subsetting cannot be done on Array datatypes.
 
-See this <a href="https://docs.hdfgroup.org/hdf5/v1_14/_l_b_datatypes.html">section</a> for more information on the Array datatype.
+See this <a href="https://docs.hdfgroup.org/hdf5/v1_14_4/_l_b_datatypes.html">section</a> for more information on the Array datatype.
 
 \subsubsection subsubsecViewToolsViewDtypes_objref Object Reference
 An Object Reference is a reference to an entire object (dataset, group, or named datatype).

doxygen/examples/FileFormat.html

@@ -36,7 +36,7 @@
 </li><li><h3><u>Background Reading:</u></h3>
 
 <dl>
-    <dt><a href="https://hdfgroup.github.io/hdf5/v1_14/_s_p_e_c.html">HDF5 File Format Specification</a>
+    <dt><a href="https://hdfgroup.github.io/hdf5/v1_14_4/_s_p_e_c.html">HDF5 File Format Specification</a>
         </dt><dd>This describes the current HDF5 file format.
 </dd></dl>
 

doxygen/examples/menus/high_level_menu.md

@@ -1,4 +1,5 @@
-<b>High-level library</b>
+## High-level Library
+
 <br />
 The high-level HDF5 library includes several sets of convenience and standard-use APIs to 
 facilitate common HDF5 operations.

fortran/src/README.md

@@ -109,11 +109,7 @@ FOR DEVELOPERS
 
   The valid KINDs for integers and reals that are stored in H5config_f.inc are used in the H5_buildiface.F90 file located in the fortran/src directory. During the build process, H5_buildiface.F90 generates all the valid F90 KIND interfaces for the following APIs: h5awrite_f, h5aread_f, h5dwrite_f, h5dread_f, h5pset_fill_value_f, h5pget_fill_value_f, h5pset_f, h5pget_f, h5pregister_f, and h5pinsert_f. These APIs can handle up to and including rank seven arrays for all the found KINDs. Again, it's important to note that no new Fortran APIs should be added to H5_buildiface.F90 since new Fortran APIs should not use F90 specification but should instead use F2003. The source file generated by H5_buildiface.F90 is H5_gen.F90, which is the Fortran module H5_GEN, Figure 1. This module is included in the HDF5 module HDF5.F90.
 
-  <figure>
-  <!-- Xfig graphic -->
-    <img src="./FortBuildFlow.svg">
-    <figcaption>Figure 1: During the configure and build phases, Fortran files are generated and compiled. This overview explains the flow steps of the build process.</figcaption>
-  </figure>
+  ![Figure 1: During the configure and build phases, Fortran files are generated and compiled. This overview explains the flow steps of the build process.](./FortBuildFlow.svg)
 
 Procedure to add a new function
 --------------------------------

release_docs/NEWSLETTER.txt

@@ -1,4 +1,4 @@
-HDF5 version 1.14.4 currently under development
+HDF5 version 1.14.4 released on 2024-04-11
 
 This is a maintenance release with a few changes and updates:
 ----------------------------------------------------------------------------

src/H5Fmodule.h

@@ -235,10 +235,10 @@
  * Note that the root group, indicated above by /, was automatically created when the file was created.
  *
  * h5dump is described on the
- * <a href="https://docs.hdfgroup.org/hdf5/v1_14/_view_tools_view.html#subsecViewToolsViewContent_h5dump">
+ * <a href="https://docs.hdfgroup.org/hdf5/v1_14_4/_view_tools_view.html#subsecViewToolsViewContent_h5dump">
  * Tools</a>
  * page under
- * <a href="https://docs.hdfgroup.org/hdf5/v1_14/_view_tools_command.html">Command-line Tools</a>.
+ * <a href="https://docs.hdfgroup.org/hdf5/v1_14_4/_view_tools_command.html">Command-line Tools</a>.
  * The HDF5 DDL grammar is described in the document \ref DDLBNF114.
  *
  * \subsection subsec_file_summary File Function Summaries
@@ -712,7 +712,7 @@
  * If the application opens an HDF5 file without both determining the driver used to create the file
  * and setting up the use of that driver, the HDF5 Library will examine the superblock and the
  * driver definition block to identify the driver.
- * See the <a href="https://hdfgroup.github.io/hdf5/v1_14/_s_p_e_c.html">HDF5 File Format Specification</a>
+ * See the <a href="https://hdfgroup.github.io/hdf5/v1_14_4/_s_p_e_c.html">HDF5 File Format Specification</a>
  * for detailed descriptions of the superblock and the driver definition block.
  *
  * \subsubsection subsubsec_file_alternate_drivers_sec2 The POSIX (aka SEC2) Driver

src/H5Ppublic.h

@@ -9031,7 +9031,7 @@ H5_DLL herr_t H5Pset_link_phase_change(hid_t plist_id, unsigned max_compact, uns
  *      must be created and maintained in the original style. This is HDF5's default
  *      behavior. If backward compatibility with pre-1.8.0 libraries is not a concern,
  *      greater efficiencies can be obtained with the new-format compact and indexed
- *      groups. See <a href="https://docs.hdfgroup.org/hdf5/v1_14/group___h5_g.html">Group
+ *      groups. See <a href="https://docs.hdfgroup.org/hdf5/v1_14_4/group___h5_g.html">Group
  *      implementations in HDF5</a> in the \ref H5G API introduction (at the bottom).\n
  *      H5Pset_local_heap_size_hint() is useful for tuning file size when files
  *      contain original-style groups with either zero members or very large

src/H5module.h

@@ -49,7 +49,7 @@
  * The <em>Abstract Data Model</em> is a conceptual model of data, data types, and data organization. The
  * abstract data model is independent of storage medium or programming environment. The
  * <em>Storage Model</em> is a standard representation for the objects of the abstract data model. The
- * <a href="https://hdfgroup.github.io/hdf5/v1_14/_s_p_e_c.html">HDF5 File Format Specification</a>
+ * <a href="https://hdfgroup.github.io/hdf5/v1_14_4/_s_p_e_c.html">HDF5 File Format Specification</a>
  * defines the storage model.
  *
  * The <em>Programming Model</em> is a model of the computing environment and includes platforms from
@@ -100,7 +100,7 @@
  * model, and stored in a storage medium. The stored objects include header blocks, free lists, data
  * blocks, B-trees, and other objects. Each group or dataset is stored as one or more header and data
  * blocks.
- * @see <a href="https://hdfgroup.github.io/hdf5/v1_14/_s_p_e_c.html">HDF5 File Format Specification</a>
+ * @see <a href="https://hdfgroup.github.io/hdf5/v1_14_4/_s_p_e_c.html">HDF5 File Format Specification</a>
  * for more information on how these objects are organized. The HDF5 library can also use other
  * libraries and modules such as compression.
  *
@@ -125,7 +125,7 @@
  * HDF5 abstract data model is up to the application developer. The application program only
  * needs to deal with the library and the abstract data model. Most applications need not consider
  * any details of the
- * <a href="https://hdfgroup.github.io/hdf5/v1_14/_s_p_e_c.html">HDF5 File Format Specification</a>
+ * <a href="https://hdfgroup.github.io/hdf5/v1_14_4/_s_p_e_c.html">HDF5 File Format Specification</a>
  * or the details of how objects of abstract data model are translated to and from storage.
  *
  * \subsection subsec_data_model_abstract The Abstract Data Model
@@ -408,7 +408,7 @@
  *
  * \subsection subsec_data_model_storage The HDF5 Storage Model
  * \subsubsection subsubsec_data_model_storage_spec The Abstract Storage Model: the HDF5 Format Specification
- * The <a href="https://hdfgroup.github.io/hdf5/v1_14/_s_p_e_c.html">HDF5 File Format Specification</a>
+ * The <a href="https://hdfgroup.github.io/hdf5/v1_14_4/_s_p_e_c.html">HDF5 File Format Specification</a>
  * defines how HDF5 objects and data are mapped to a linear
  * address space. The address space is assumed to be a contiguous array of bytes stored on some
  * random access medium. The format defines the standard for how the objects of the abstract data

test/API/README.md

@@ -1,7 +1,7 @@
 # HDF5 API Tests
 
 This directory contains several test applications that exercise HDF5's
-public API and serve as regression tests for HDF5 [VOL Connectors](https://docs.hdfgroup.org/hdf5/v1_14/_h5_v_l__u_g.html).
+public API and serve as regression tests for HDF5 [VOL Connectors](https://docs.hdfgroup.org/hdf5/v1_14_4/_h5_v_l__u_g.html).
 
 ## Build Process and options
 
@@ -42,7 +42,7 @@ Currently unsupported
 
 These API tests currently only support usage with the native HDF5 VOL connector and HDF5 VOL
 connectors that can be loaded dynamically as a plugin. For information on how to build a VOL
-connector in this manner, refer to section 2.3 of the [HDF5 VOL Connector Author Guide](https://docs.hdfgroup.org/hdf5/v1_14/_v_o_l__connector.html).
+connector in this manner, refer to section 2.3 of the [HDF5 VOL Connector Author Guide](https://docs.hdfgroup.org/hdf5/v1_14_4/_v_o_l__connector.html).
 
 TODO: section on building VOL connectors alongside HDF5 for use with tests