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 <diogoteles@google.com>

* feat: enable dependabot for monthly updates on GHA

Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com>

---------

Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com>

* 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 <qkoziol@amazon.com>

* 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)

2 files changed, 5 insertions, 5 deletions

diff --git a/utils/tools/h5dwalk/CMakeLists.txt b/utils/tools/h5dwalk/CMakeLists.txt
index 9e4eb6d..f0611e0 100644
--- a/utils/tools/h5dwalk/CMakeLists.txt
+++ b/utils/tools/h5dwalk/CMakeLists.txt
@@ -7,9 +7,9 @@ project (HDF5_UTILS_TOOLS_H5DWALK C)
 if (BUILD_STATIC_LIBS)
   add_executable (h5dwalk ${HDF5_UTILS_TOOLS_H5DWALK_SOURCE_DIR}/h5dwalk.c)
 #  add_custom_target(generate_demo ALL
-#    DEPENDS "${HDF5_TOOLS_DIR}/test/demo_destfiles.test"
+#    DEPENDS "${HDF5_TOOLS_ROOT_DIR}/test/demo_destfiles.test"
 #  )
-  target_include_directories (h5dwalk PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};${CIRCLE_INCLUDE_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5dwalk PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};${CIRCLE_INCLUDE_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5dwalk PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5dwalk STATIC)
   target_link_libraries (h5dwalk PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET} ${MFU_LIBRARY} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:MPI::MPI_C>")
@@ -21,7 +21,7 @@ endif ()
 
 if (BUILD_SHARED_LIBS)
   add_executable (h5dwalk-shared ${HDF5_UTILS_TOOLS_H5DWALK_SOURCE_DIR}/h5dwalk.c)
-  target_include_directories (h5dwalk-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};${CIRCLE_INCLUDE_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5dwalk-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};${CIRCLE_INCLUDE_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5dwalk-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5dwalk-shared SHARED)
   target_link_libraries (h5dwalk-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET} ${MFU_LIBRARY} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:MPI::MPI_C>")
diff --git a/utils/tools/test/h5dwalk/CMakeLists.txt b/utils/tools/test/h5dwalk/CMakeLists.txt
index 530bed8..a27190c 100644
--- a/utils/tools/test/h5dwalk/CMakeLists.txt
+++ b/utils/tools/test/h5dwalk/CMakeLists.txt
@@ -3,9 +3,9 @@ project (HDF5_TOOLS_TEST_H5DWALK)
 
 if (HDF5_BUILD_PARALLEL_TOOLS)
   add_custom_command(
-    OUTPUT ${HDF5_TOOLS_DIR}/test/demo_destfiles.test
+    OUTPUT ${HDF5_TOOLS_ROOT_DIR}/test/demo_destfiles.test
     COMMAND bash -c ${HDF5_TOOLS_SRC_H5DWALK_SOURCE_DIR}/copy_demo_files.sh
-    ARGS ${HDF5_TOOLS_DIR}/test ${CMAKE_BINARY_DIR}/bin
+    ARGS ${HDF5_TOOLS_ROOT_DIR}/test ${CMAKE_BINARY_DIR}/bin
     DEPENDS ${HDF5_TOOLS_SRC_H5DWALK_SOURCE_DIR}/copy_demo_files.sh
   )
 endif ()