Merge remote-tracking branch 'origin/develop' into locking_protocol

.github/workflows/linkchecker.yml

@@ -0,0 +1,47 @@
+name: linkchecker
+
+on:
+  workflow_dispatch:
+  push:
+  pull_request:
+    branches: [ develop ]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref && github.ref || github.run_id }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: get
+        uses: actions/checkout@v4
+
+      - name: install
+        run: |
+          sudo apt update -y
+          sudo apt install -y libunwind-dev
+          sudo apt install -y graphviz
+          sudo apt install -y --no-install-recommends doxygen
+          sudo apt install -y cmake
+          sudo apt install -y texlive-full
+          sudo apt install -y texlive-fonts-extra
+          sudo apt install -y texlive-latex-extra
+          pip3 install linkchecker
+
+      - name: build
+        run: |
+          mkdir build
+          cd build
+          cmake -DHDF5_BUILD_DOC:BOOL=ON ..
+          make doxygen
+
+      - name: check
+        run: |
+          cd build/hdf5lib_docs/html
+          linkchecker --check-extern ./index.html
+        continue-on-error: true
+

.github/workflows/release-files.yml

@@ -221,7 +221,7 @@ jobs:
       - name: PreRelease tag
         id: create_prerelease
         if: ${{ (inputs.use_environ == 'snapshots') }}
-        uses: softprops/action-gh-release@e7a8f85e1c67a31e6ed99a94b41bd0b71bbee6b8 # v2.0.9
+        uses: softprops/action-gh-release@01570a1f39cb168c169c802c3bceb9e93fb10974 # v2.1.0
         with:
           tag_name: "${{ inputs.use_tag }}"
           prerelease: true
@@ -249,7 +249,7 @@ jobs:
       - name: Release tag
         id: create_release
         if: ${{ (inputs.use_environ == 'release') }}
-        uses: softprops/action-gh-release@e7a8f85e1c67a31e6ed99a94b41bd0b71bbee6b8 # v2.0.9
+        uses: softprops/action-gh-release@01570a1f39cb168c169c802c3bceb9e93fb10974 # v2.1.0
         with:
           tag_name: "${{ inputs.use_tag }}"
           prerelease: false

.github/workflows/scorecard.yml

@@ -67,6 +67,6 @@ jobs:
 
       # Upload the results to GitHub's code scanning dashboard.
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@662472033e021d55d94146f66f6058822b0b39fd # v3.27.0
+        uses: github/codeql-action/upload-sarif@f09c1c0a94de965c15400f5634aa42fac8fb8f88 # v3.27.5
         with:
           sarif_file: results.sarif

config/cmake/hdf5-config.cmake.in

@@ -88,6 +88,7 @@ if (${HDF5_PACKAGE_NAME}_ENABLE_PARALLEL)
   set (${HDF5_PACKAGE_NAME}_PARALLEL_FILTERED_WRITES @PARALLEL_FILTERED_WRITES@)
   set (${HDF5_PACKAGE_NAME}_LARGE_PARALLEL_IO        @LARGE_PARALLEL_IO@)
 
+  enable_language(C) # for MPI::MPI_C
   find_package(MPI QUIET REQUIRED)
 endif ()
 

doxygen/dox/Overview.dox

@@ -21,7 +21,7 @@ documents cover a mix of tasks, concepts, and reference, to help a specific
 <em>audience</em> succeed.
 
 \par Offline reading
-     You can <a href="https://\RELURL/v1_14/v1_14_5/hdf5-1.14.5.doxygen.zip">download</a> it as an archive for offline reading.
+     You can <a href="https://\RELURL/v1_14/v1_14_5/downloads/hdf5-1.14.5.doxygen.zip">download</a> it as an archive for offline reading.
 
 \par ToDo List
      There is plenty of <a href="./todo.html">unfinished business</a>.

doxygen/dox/TechnicalNotes.dox

@@ -1063,7 +1063,161 @@ been used at the lowest level to process the request.
 
 /** \page APPDBG Debugging HDF5 Applications
 
-\htmlinclude DebuggingHDF5Applications.html
+\section sec_adddbg_intro Introduction
+The HDF5 library contains a number of debugging features to make programmers' lives
+easier including the ability to print detailed error messages, check invariant
+conditions, display timings and other statistics.
+
+\subsection subsec_adddbg_intro_err Error Messages
+Error messages are normally displayed automatically on the standard error stream and
+include a stack trace of the library including file names, line numbers, and function
+names. The application has complete control over how error messages are displayed and
+can disable the display on a permanent or temporary basis. Refer to the documentation
+ for the H5E error handling package.
+
+\subsection subsec_adddbg_intro_invar Invariant Conditions
+Unless NDEBUG is defined during compiling, the library will include code to verify that
+invariant conditions have the expected values. When a problem is detected the library will
+display the file and line number within the library and the invariant condition that
+failed. A core dump may be generated for post mortem debugging. The code to perform these
+checks can be included on a per-package bases.
+
+\subsection subsec_adddbg_intro_stats Timings and Statistics
+The library can be configured to accumulate certain statistics about things like cache
+performance, datatype conversion, data space conversion, and data filters. The code is
+included on a per-package basis and enabled at runtime by an environment variable.
+
+\subsection subsec_adddbg_intro_trace API Tracing
+All API calls made by an application can be displayed and include formal argument names
+and actual values and the function return value. This code is also conditionally included
+at compile time and enabled at runtime.
+
+The statistics and tracing can be displayed on any output stream (including streams opened by
+the shell) with output from different packages even going to different streams.
+
+\section sec_adddbg_msg Error Messages
+By default any API function that fails will print an error stack to the standard error stream.
+\code
+HDF5-DIAG: Error detected in thread 0.  Back trace follows.
+  #000: H5F.c line 1245 in H5Fopen(): unable to open file
+    major(04): File interface
+    minor(10): Unable to open file
+  #001: H5F.c line 846 in H5F_open(): file does not exist
+    major(04): File interface
+    minor(10): Unable to open file
+\endcode
+The error handling package (H5E) is described elsewhere.
+
+\section sec_adddbg_invars Invariant Conditions
+To include checks for invariant conditions the library should be configured
+with --disable-production, the default for versions before 1.2. The library
+designers have made every attempt to handle error conditions gracefully but
+an invariant condition assertion may fail in certain cases. The output from
+a failure usually looks something like this:
+\code
+Assertion failed: H5.c:123: i<NELMTS(H5_debug_g)
+IOT Trap, core dumped.
+\endcode
+
+\section sec_adddbg_stats Timings and Statistics
+Code to accumulate statistics is included at compile time by using the --enable-debug
+configure switch. The switch can be followed by an equal sign and a comma-separated
+list of package names or else a default list is used.
+<table>
+<tr>
+<th><strong>Name</strong>
+</th>
+<th><strong>Default</strong>
+</th>
+<th><strong>Description</strong>
+</th>
+</tr>
+<tr>
+<td>a</td><td>No</td><td>Attributes</td>
+</tr>
+<tr>
+<td>ac</td><td>Yes</td><td>Meta data cache</td>
+</tr>
+<tr>
+<td>b</td><td>Yes</td><td>B-Trees</td>
+</tr>
+<tr>
+<td>d</td><td>Yes</td><td>Datasets</td>
+</tr>
+<tr>
+<td>e</td><td>Yes</td><td>Error handling</td>
+</tr>
+<tr>
+<td>f</td><td>Yes</td><td>Files</td>
+</tr>
+<tr>
+<td>g</td><td>Yes</td><td>Groups</td>
+</tr>
+<tr>
+<td>hg</td><td>Yes</td><td>Global heap</td>
+</tr>
+<tr>
+<td>hl</td><td>No</td><td>Local heaps</td>
+</tr>
+<tr>
+<td>i</td><td>Yes</td><td>Interface abstraction</td>
+</tr>
+<tr>
+<td>mf</td><td>No</td><td>File memory management</td>
+</tr>
+<tr>
+<td>mm</td><td>Yes</td><td>Library memory management</td>
+</tr>
+<tr>
+<td>o</td><td>No</td><td>Object headers and messages</td>
+</tr>
+<tr>
+<td>p</td><td>Yes</td><td>Property lists</td>
+</tr>
+<tr>
+<td>s</td><td>Yes</td><td>Data spaces</td>
+</tr>
+<tr>
+<td>t</td><td>Yes</td><td>Datatypes</td>
+</tr>
+<tr>
+<td>v</td><td>Yes</td><td>Vectors</td>
+</tr>
+<tr>
+<td>z</td><td>Yes</td><td>Raw data filters</td>
+</tr>
+</table>
+
+In addition to including the code at compile time the application must enable each package at
+runtime. This is done by listing the package names in the HDF5_DEBUG environment variable. That
+variable may also contain file descriptor numbers (the default is '2') which control the output
+for all following packages up to the next file number. The word 'all' refers to all packages. Any
+word my be preceded by a minus sign to turn debugging off for the package.
+
+\subsection subsec_adddbg_stats_sample Sample debug specifications
+<table>
+<tr>
+<td>all
+</td>
+<td>This causes debugging output from all packages to be sent to the standard error stream.
+</td>
+</tr>
+<tr>
+<td>all -t -s
+</td>
+<td>Debugging output for all packages except datatypes and data spaces will appear on the standard error stream.
+</td>
+</tr>
+<tr>
+<td>-all ac 255 t,s
+</td>
+<td>This disables all debugging even if the default was to debug something, then output
+from the meta data cache is send to the standard error stream and output from data types
+and spaces is sent to file descriptor 255 which should be redirected by the shell.
+</td>
+</tr>
+</table>
+The components of the HDF5_DEBUG value may be separated by any non-lowercase letter.
 
 */
 

doxygen/dox/UsersGuide.dox

@@ -335,6 +335,23 @@
 
 \ref sec_map
 
+\section sec_hl HDF5 High Level APIs
+\li \ref H5DO_UG
+    <ul>
+        <li> \ref sec_hldo_direct_chunk
+    </ul>
+\li \ref H5DS_UG
+    <ul>
+        <li> \ref sec_dim_scales_stand
+        <li> \ref sec_dim_scales_concept
+        <li> \ref sec_dim_scales_spec
+        <li> \ref sec_dim_scales_api
+    </ul>
+\li \ref H5IM_UG
+\li \ref H5LT_UG
+\li \ref H5TB_UG
+\li \ref H5PT_UG
+
 \ref sec_cltools
 \li \ref H5TOOL_CP_UG
 \li \ref H5TOOL_DF_UG

doxygen/dox/VOLConnGuide.dox

@@ -191,7 +191,8 @@ are for connector testing and should not be found in the wild. Values of 512 to
 connectors.
 
 As is the case with HDF5 filters, The HDF Group can assign you an official VOL connector value. Please
-contact <a href="[email protected]">[email protected]</a> for help with this. We currently do not register connector names, though the
+contact <a href="mailto:[email protected]">[email protected]</a> for help with this. We currently do not 
+register connector names, though the
 name you've chosen will appear on the registered VOL connectors page.
 
 As noted above, registered VOL connectors will be listed at: