Sync 1.14 branch with develop (#3923)

* Fix build error on freebsd (#3883)

Fixes:

checking for config freebsd12.1... no
checking for config freebsd... found
compiler '/home/svcpetsc/petsc-hash-pkgs/39f577/bin/mpicc' is GNU gcc-9.2.0
compiler '/home/svcpetsc/petsc-hash-pkgs/39f577/bin/mpif90' is GNU gfortran-9.2.0
stdout: .: cannot open ./config/classic-fflags: No such file or directory

* Correct CMake command and example packaging (#3888)

* Feat: Hashpin sensitive dependencies on GitHub Actions and enable Dependabot to update them monthly (#3892)

* feat: hashpin sensitive dependencies on GHAs

Signed-off-by: Diogo Teles Sant'Anna <[email protected]>

* feat: enable dependabot for monthly updates on GHA

Signed-off-by: Diogo Teles Sant'Anna <[email protected]>

---------

Signed-off-by: Diogo Teles Sant'Anna <[email protected]>

* Some changes to portal links when they could be found on docs.hdfgroup.org, and changed the helpdesk link to help.hdfgroup.org (#3893)

* Updated some portal links to go directly to docs.hdfgroup. 

* Fixed some portal and help desk links

* Add variable option syncing for examples (#3885)

* Add period(.) at the end of the sentence for consistency. (#3897)

* Remove redundant backslash character from comment. (#3899)

* Disable doxygen as errors for netcdf (#3900)

* disable building doxygen for netcdf test

* Doc versions (#3903)

* Added missing \since tags to H5D.

* Committing clang-format changes

* Fixed H5T version info.

* Committing clang-format changes

* Added missing version info to H5E.

* Committing clang-format changes

* Added version info to H5F public APIs.

* Committing clang-format changes

* Added missing H5Z public API version info.

* Added missing version info to H5G public APIs

* Added missing version info to H5I public API.

* Added missing version info to H5 public APIs

* Committing clang-format changes

* Added missing version info to H5P public APIs

* Added missing version info to H5R public APIs

* Fix comment error.

* Committing clang-format changes

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Change Trouble Shooting to Troubleshooting (#3905)

* Implement optimized support for vector I/O in Subfiling VFD (#3896)

Vector I/O requests are now processed within a single
set of I/O call batches, rather than each I/O vector
entry (tuple constructed from the types, addrs, sizes
and bufs arrays) being processed individually. This allows I/O to be
more efficiently parallelized among the I/O concentrator processes
during large I/O requests.

* Fixed some calculations and add test cases for issues spotted from review

* Removed a variable that was compensating for previous miscalculations

* Add 'warning density' computation to the warnhist script (#3910)

* Add 'warning density' computation to the warnhist script, along with several
cleanups to it.   Add "--enable-show-all-warnings" configure (and CMake)
option to disable compiler diagnostic suppression (and therefore show all the
otherwise suppressed compiler diagnostics), disabled by default.  Clean up
a buncn of misc. warnings.

Signed-off-by: Quincey Koziol <[email protected]>

* Added H5Fdelete_f with test (#3912)

* New Fortran Examples added (#3916)

* added subfiling example

* Added filtered writes with no selection example

* Version and space corrections.

* Restore H5_VERSION definition in configure.ac.

* renamed defined H5_VERS* to avoid conflicts (#3926)

.github/workflows/release-files.yml

@@ -174,7 +174,7 @@ jobs:
               ls ${{ runner.workspace }}
 
       - name: branch-only-docs
-        uses: peaceiris/actions-gh-pages@373f7f263a76c20808c831209c920827a82a2847 # v3
+        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

HDF5Examples/CMakeLists.txt

@@ -159,7 +159,7 @@ if (${H5_LIBVER_DIR} GREATER 16)
       endif ()
 
       configure_file (${H5EX_F90_SRC_DIR}/H5D/h5_version.h.in ${PROJECT_BINARY_DIR}/FORTRAN/H5D/h5_version.h @ONLY)
-      configure_file (${H5EX_F90_SRC_DIR}/H5G/h5_version.h.in ${PROJECT_BINARY_DIR}/FORTRAN/H5G/h5_version.h @ONLY)
+      configure_file (${H5EX_F90_SRC_DIR}/H5D/h5_version.h.in ${PROJECT_BINARY_DIR}/FORTRAN/H5G/h5_version.h @ONLY)
     else ()
       set (HDF_BUILD_FORTRAN OFF CACHE BOOL "Build examples FORTRAN support" FORCE)
     endif ()

HDF5Examples/FORTRAN/H5PAR/CMakeLists.txt

@@ -12,6 +12,7 @@ project (HDF5Examples_FORTRAN_H5PAR Fortran)
 INCLUDE_DIRECTORIES (
     ${CMAKE_Fortran_MODULE_DIRECTORY}${HDF_MOD_EXT}
     ${PROJECT_BINARY_DIR}
+    ${HDF5_F90_BINARY_DIR}
     ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}
 )
 

HDF5Examples/FORTRAN/H5PAR/Fortran_sourcefiles.cmake

@@ -9,3 +9,14 @@ set (examples
   ph5_f90_hyperslab_by_pattern
   ph5_f90_hyperslab_by_chunk
 )
+
+if (HDF5_ENABLE_SUBFILING_VFD)
+  set (examples ${examples}
+    ph5_f90_subfiling
+  )
+endif()
+if (HDF5_VERSION_STRING VERSION_GREATER_EQUAL "1.14.4")
+  set (examples ${examples}
+    ph5_f90_filtered_writes_no_sel
+  )
+endif()

HDF5Examples/FORTRAN/H5PAR/ph5_f90_dataset.F90

@@ -1,10 +1,9 @@
      PROGRAM DATASET
 
      USE HDF5 ! This module contains all necessary modules
+     USE MPI
 
      IMPLICIT NONE
-
-     INCLUDE 'mpif.h'
      CHARACTER(LEN=10), PARAMETER :: filename = "sds.h5"  ! File name
      CHARACTER(LEN=8), PARAMETER :: dsetname = "IntArray" ! Dataset name
 

HDF5Examples/FORTRAN/H5PAR/ph5_f90_file_create.F90

@@ -5,10 +5,10 @@
      PROGRAM FILE_CREATE
 
      USE HDF5 ! This module contains all necessary modules
+     USE MPI
 
      IMPLICIT NONE
 
-     INCLUDE 'mpif.h'
      CHARACTER(LEN=10), PARAMETER :: filename = "sds.h5"  ! File name
 
      INTEGER(HID_T) :: file_id       ! File identifier