Merge branch 'HDFGroup:develop' into develop

README.md

@@ -2,13 +2,12 @@ HDF5 version 1.15.0 currently under development
 
 ![HDF5 Logo](doxygen/img/HDF5.png)
 
-[![develop build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/main.yml?branch=develop&label=develop)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Adevelop)
-[![HDF-EOS5 build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/hdfeos5.yml?branch=develop&label=HDF-EOS5)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Adevelop)
-[![netCDF build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/netcdf.yml?branch=develop&label=netCDF)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Adevelop)
-[![h5py build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/h5py.yml?branch=develop&label=h5py)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Adevelop)
-[![CVE regression](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/cve.yml?branch=develop&label=CVE)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Adevelop)
-[![1.14 build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/main.yml?branch=hdf5_1_14&label=1.14)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Ahdf5_1_14)
-[![1.12 build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/main.yml?branch=hdf5_1_12&label=1.12)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Ahdf5_1_12)
+[![develop build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/main.yml?branch=develop&label=develop)](https://github.com/HDFGroup/hdf5/actions/workflows/main.yml?query=branch%3Adevelop)
+[![HDF-EOS5 build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/hdfeos5.yml?branch=develop&label=HDF-EOS5)](https://github.com/HDFGroup/hdf5/actions/workflows/hdfeos5.yml?query=branch%3Adevelop)
+[![netCDF build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/netcdf.yml?branch=develop&label=netCDF)](https://github.com/HDFGroup/hdf5/actions/workflows/netcdf.yml?query=branch%3Adevelop)
+[![h5py build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/h5py.yml?branch=develop&label=h5py)](https://github.com/HDFGroup/hdf5/actions/workflows/h5py.yml?query=branch%3Adevelop)
+[![CVE regression](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/cve.yml?branch=develop&label=CVE)](https://github.com/HDFGroup/hdf5/actions/workflows/cve.yml?query=branch%3Adevelop)
+[![1.14 build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/main.yml?branch=hdf5_1_14&label=1.14)](https://github.com/HDFGroup/hdf5/actions/workflows/main.yml?query=branch%3Ahdf5_1_14)
 [![BSD](https://img.shields.io/badge/License-BSD-blue.svg)](https://github.com/HDFGroup/hdf5/blob/develop/COPYING)
 
 [HPC configure/build/test results](https://my.cdash.org/index.php?project=HDF5)
@@ -87,8 +86,6 @@ are tentative.
 
 | Release | New Features |
 | ------- | ------------ |
-| 1.12.3 | CVE fixes, performance improvements, H5Dchunk\_iter(), last HDF5 1.12 release |
-| 1.14.3 | CVE-free!, better cross-compile support |
 | 1.14.4 | S3 VFD improvements |
 | TBD | VFD SWMR |
 | 2.0.0 | TBD |

config/cmake/examples/HDF5_Examples.cmake.in

@@ -53,7 +53,7 @@ set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCTEST_CONFIGURATION_TYPE:STRING=${
 
 if(NOT DEFINED INSTALLDIR)
   if(WIN32)
-    set(INSTALLDIR "%ProgramFiles%/HDF_Group/@HDF5_PACKAGE_NAME@/@HDF5_PACKAGE_VERSION@")
+    set(INSTALLDIR "\"%ProgramFiles%/HDF_Group/@HDF5_PACKAGE_NAME@/@HDF5_PACKAGE_VERSION@\"")
   else()
     set(INSTALLDIR "@CMAKE_INSTALL_PREFIX@")
   endif()
@@ -78,6 +78,7 @@ set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DSITE:STRING=${CTEST_SITE} -DBUILDN
 
 ###############################################################################################################
 set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ROOT:PATH=${INSTALLDIR}")
+set (ENV{HDF5_ROOT} "${INSTALLDIR}")
 if(WIN32)
   set(SITE_OS_NAME "Windows")
   set(CTEST_BINARY_NAME ${CTEST_SOURCE_NAME}\\build)
@@ -98,11 +99,11 @@ endif()
 set(ENV{HDF5_PLUGIN_PATH} "${INSTALLDIR}/lib/plugin")
 set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACKAGE_NAME:STRING=@HDF5_PACKAGE@@HDF_PACKAGE_EXT@")
 ### use a toolchain file (supported everywhere)       ####
-if(NOT DEFINED CTEST_TOOLCHAIN_FILE)
-  set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=@CTEST_TOOLCHAIN_FILE@")
-else()
-  set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=${CTEST_TOOLCHAIN_FILE}")
-endif()
+#if(NOT DEFINED CTEST_TOOLCHAIN_FILE)
+#  set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=@CTEST_TOOLCHAIN_FILE@")
+#else()
+#  set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=${CTEST_TOOLCHAIN_FILE}")
+#endif()
 
 ###############################################################################################################
 # For any comments please contact [email protected]

configure.ac

@@ -4285,11 +4285,5 @@ if test "X$HDF_FORTRAN" = "Xyes"; then
   esac
 fi
 
-## HDF5 configure code created by autotools with gcc 4.9.2 is adding problematic
-## linker flags:  -l with no library name; -l <libname>, specifically gfortran or m.
-## This sed script corrects "-l <libname>" first and then "-l " with no library name.
-## If the order is not preserved, all instances of "-l " will be removed.
-sed -e '/^postdeps/ s/-l \([a-zA-Z]\)/-l\1/g' -e '/^postdeps/ s/-l //g' -i libtool
-
 ## show the configure settings
 cat src/libhdf5.settings

fortran/src/CMakeLists.txt

@@ -37,10 +37,25 @@ if (H5_HAVE_PARALLEL)
 endif ()
 
 set (CMAKE_H5_HAVE_FLOAT128 0)
-if (HAVE_FLOAT128)
+if (H5_HAVE_FLOAT128)
   set (CMAKE_H5_HAVE_FLOAT128 1)
 endif ()
 
+set (CMAKE_H5_FORTRAN_HAVE_STORAGE_SIZE 0)
+if (H5_FORTRAN_HAVE_STORAGE_SIZE)
+  set (CMAKE_H5_FORTRAN_HAVE_STORAGE_SIZE 1)
+endif ()
+
+set (CMAKE_H5_FORTRAN_HAVE_SIZEOF 0)
+if (H5_FORTRAN_HAVE_SIZEOF)
+  set (CMAKE_H5_FORTRAN_HAVE_SIZEOF 1)
+endif ()
+
+set (CMAKE_H5_FORTRAN_HAVE_C_SIZEOF 0)
+if (H5_FORTRAN_HAVE_C_SIZEOF)
+  set (CMAKE_H5_FORTRAN_HAVE_C_SIZEOF 1)
+endif ()
+
 configure_file (${HDF5_F90_SRC_SOURCE_DIR}/H5config_f.inc.cmake ${HDF5_F90_BINARY_DIR}/H5config_f.inc @ONLY)
 configure_file (${HDF5_F90_SRC_SOURCE_DIR}/H5fort_type_defines.h.cmake ${HDF5_F90_BINARY_DIR}/H5fort_type_defines.h @ONLY)
 

fortran/src/H5_ff.F90

@@ -996,7 +996,7 @@ INTEGER(HID_T) FUNCTION h5kind_to_type(ikind, flag) RESULT(h5_type)
           h5_type = H5T_NATIVE_REAL_C_LONG_DOUBLE
 #endif
 #if H5_PAC_FC_MAX_REAL_PRECISION > 28
-#if H5_HAVE_FLOAT128 == 1
+#ifdef H5_HAVE_FLOAT128
        ELSE
           h5_type = H5T_NATIVE_FLOAT_128
 #endif

fortran/src/H5config_f.inc.cmake

@@ -36,13 +36,28 @@
 #endif
 
 ! Define if the intrinsic function STORAGE_SIZE exists
-#cmakedefine H5_FORTRAN_HAVE_STORAGE_SIZE @H5_FORTRAN_HAVE_STORAGE_SIZE@
+#cmakedefine01 CMAKE_H5_FORTRAN_HAVE_STORAGE_SIZE
+#if CMAKE_H5_FORTRAN_HAVE_STORAGE_SIZE == 0
+#undef H5_FORTRAN_HAVE_STORAGE_SIZE
+#else
+#define H5_FORTRAN_HAVE_STORAGE_SIZE
+#endif
 
 ! Define if the intrinsic function SIZEOF exists
-#cmakedefine H5_FORTRAN_HAVE_SIZEOF @H5_FORTRAN_HAVE_SIZEOF@
+#cmakedefine01 CMAKE_H5_FORTRAN_HAVE_SIZEOF
+#if CMAKE_H5_FORTRAN_HAVE_SIZEOF == 0
+#undef H5_FORTRAN_HAVE_SIZEOF
+#else
+#define H5_FORTRAN_HAVE_SIZEOF
+#endif
 
 ! Define if the intrinsic function C_SIZEOF exists
-#cmakedefine H5_FORTRAN_HAVE_C_SIZEOF @H5_FORTRAN_HAVE_C_SIZEOF@
+#cmakedefine01 CMAKE_H5_FORTRAN_HAVE_C_SIZEOF
+#if CMAKE_H5_FORTRAN_HAVE_C_SIZEOF == 0
+#undef H5_FORTRAN_HAVE_C_SIZEOF
+#else
+#define H5_FORTRAN_HAVE_C_SIZEOF
+#endif
 
 ! Define if the intrinsic function C_LONG_DOUBLE exists
 #define H5_FORTRAN_HAVE_C_LONG_DOUBLE @H5_FORTRAN_HAVE_C_LONG_DOUBLE@
@@ -63,7 +78,12 @@
 #define H5_PAC_FC_MAX_REAL_PRECISION @H5_PAC_FC_MAX_REAL_PRECISION@
 
 ! If C has quad precision
-#cmakedefine H5_HAVE_FLOAT128 @H5_HAVE_FLOAT128@
+#cmakedefine01 CMAKE_H5_HAVE_FLOAT128
+#if CMAKE_H5_HAVE_FLOAT128 == 0
+#undef H5_HAVE_FLOAT128
+#else
+#define H5_HAVE_FLOAT128
+#endif
 
 ! Define if INTEGER*16 is available
 #define H5_HAVE_Fortran_INTEGER_SIZEOF_16 @H5_HAVE_Fortran_INTEGER_SIZEOF_16@

release_docs/RELEASE.txt

@@ -835,6 +835,16 @@ Bug Fixes since HDF5-1.14.0 release
 
     Configuration
     -------------
+    - Removed an Autotools configure hack that causes problems on MacOS
+
+      A sed line in configure.ac was added in the past to paper over some
+      problems with older versions of the Autotools that would add incorrect
+      linker flags. This hack is not needed with recent versions of the
+      Autotools and the sed line errors on MacOS (though this was a silent
+      error that didn't break the build) so the hack has been removed.
+
+      Fixes GitHub issue #3843
+
     - Fixed an issue where the h5tools_test_utils test program was being
       installed on the system for Autotools builds of HDF5
 

src/H5Lpublic.h

@@ -260,9 +260,13 @@ H5_DLL herr_t H5Lcopy(hid_t src_loc, const char *src_name, hid_t dst_loc, const
  *          location and name, respectively, of the new hard link.
  *
  *          \p cur_name and \p dst_name are interpreted relative to \p cur_loc
- *          and \p dst_loc, respectively. If \p cur_loc and \p dst_loc are the
- *          same location, the HDF5 macro #H5L_SAME_LOC can be used for either
- *          parameter (but not both).
+ *          and \p dst_loc, respectively. If a given name begins with \c /,
+ *          then it will be interpreted as absolute path in the file.
+ *          The names of the created links will be the last element of
+ *          each provided path. Prior elements in each path are used to
+ *          locate the parent groups of each new link. If \p cur_loc and
+ *          \p dst_loc are the same location, the HDF5 macro
+ *          #H5L_SAME_LOC can be used for either parameter (but not both).
  *
  *          \p lcpl_id and \p lapl_id are the link creation and access property
  *          lists associated with the new link.
@@ -321,8 +325,10 @@ H5_DLL herr_t H5Lcreate_hard_async(hid_t cur_loc_id, const char *cur_name, hid_t
  *
  *          \p link_loc_id and \p link_name specify the location and name,
  *          respectively, of the new soft link. \p link_name is interpreted
- *          relative to \p link_loc_id and must contain only the name of the soft
- *          link; \p link_name may not contain any additional path elements.
+ *          as a path relative to \p link_loc_id, or an absolute path if it
+ *          begins with \c /. The name of the created link will be the last
+ *          element of the provided path. Prior elements in the path are
+ *          used to locate the parent group of the new link.
  *
  *          If \p link_loc_id is a group identifier, the object pointed to by
  *          \p link_name will be accessed as a member of that group. If
@@ -1190,7 +1196,11 @@ H5_DLL herr_t H5Lvisit_by_name2(hid_t loc_id, const char *group_name, H5_index_t
  *          named \p link_name at the location specified in \p link_loc_id with
  *          user-specified data \p udata.
  *
- *          \p link_name is interpreted relative to \p link_loc_id.
+ *          \p link_name is interpreted relative to \p link_loc_id. If
+ *          \p link_name begins with \c /, then it will be interpreted as
+ *          an absolute path in the file. The name of the created link
+ *          will be the last element of the provided path. Prior elements
+ *          in the path are used to locate the parent group of the new link.
  *
  *          Valid values for the link class of the new link, \p link_type,
  *          include #H5L_TYPE_EXTERNAL and any user-defined link classes that
@@ -1307,7 +1317,10 @@ H5_DLL herr_t H5Lunpack_elink_val(const void *ext_linkval /*in*/, size_t link_si
  *
  *          \p link_loc_id and \p link_name specify the location and name,
  *          respectively, of the new link. \p link_name is interpreted relative
- *          to \p link_loc_id.
+ *          to \p link_loc_id. If \p link_name begins with \c /, then it is
+ *          interpreted as an absolute path in the file. The name of the created
+ *          link will be the last element of the provided path. Prior elements in
+ *          the path are used to locate the parent group of the new link.
  *
  *          \p lcpl_id is the link creation property list used in creating the
  *          new link.