Accepting request 955494 from home:badshah400:branches:science

* Update to version 1.10.8.
* Minor rebase of patches to apply cleanly.

OBS-URL: https://build.opensuse.org/request/show/955494
OBS-URL: https://build.opensuse.org/package/show/science/hdf5?expand=0&rev=145

PPC64LE-Fix-long-double-handling.patch

@@ -11,10 +11,10 @@ Signed-off-by: Egbert Eich <eich@suse.com>
  hdf5-1.10.1/test/dt_arith.c                | 26 ++++++++++++++++++++++++--
  2 files changed, 40 insertions(+), 2 deletions(-)
 
-Index: hdf5-1.10.7/config/cmake/ConversionTests.c
+Index: hdf5-1.10.8/config/cmake/ConversionTests.c
 ===================================================================
---- hdf5-1.10.7.orig/config/cmake/ConversionTests.c
-+++ hdf5-1.10.7/config/cmake/ConversionTests.c
+--- hdf5-1.10.8.orig/config/cmake/ConversionTests.c
++++ hdf5-1.10.8/config/cmake/ConversionTests.c
 @@ -34,6 +34,14 @@ int HDF_NO_UBSAN main(void)
      unsigned char       s2[8];
      int                 ret = 1;
@@ -45,15 +45,15 @@ Index: hdf5-1.10.7/config/cmake/ConversionTests.c
      if(sizeof(long double) == 16) {
          /*make sure the long double type is the same as the failing type
           *which has 16 bytes in size and 11 bits of exponent.  If it is,
-Index: hdf5-1.10.7/test/dt_arith.c
+Index: hdf5-1.10.8/test/dt_arith.c
 ===================================================================
---- hdf5-1.10.7.orig/test/dt_arith.c
-+++ hdf5-1.10.7/test/dt_arith.c
-@@ -3045,7 +3045,18 @@ test_conv_flt_1 (const char *name, int r
-                         buf, saved, nelmts);
- #if H5_SIZEOF_LONG_DOUBLE!=H5_SIZEOF_DOUBLE && H5_SIZEOF_LONG_DOUBLE!=0
-             } else if(src_type == FLT_LDOUBLE) {
--                 INIT_FP_SPECIAL(src_size, src_nbits, sendian, LDBL_MANT_DIG, dst_size,
+--- hdf5-1.10.8.orig/test/dt_arith.c
++++ hdf5-1.10.8/test/dt_arith.c
+@@ -3040,7 +3040,18 @@ test_conv_flt_1(const char *name, int ru
+ #if H5_SIZEOF_LONG_DOUBLE != H5_SIZEOF_DOUBLE && H5_SIZEOF_LONG_DOUBLE != 0
+             }
+             else if (src_type == FLT_LDOUBLE) {
+-                INIT_FP_SPECIAL(src_size, src_nbits, sendian, LDBL_MANT_DIG, dst_size, buf, saved, nelmts);
 +		 size_t mant_dig = LDBL_MANT_DIG;
 +		 if (mant_dig >= src_nbits) {
 +		     /* This happens for IBM long double in little endian.
@@ -65,14 +65,14 @@ Index: hdf5-1.10.7/test/dt_arith.c
 +			override the mantissa size.  */
 +		     mant_dig = 52;
 +		 }
-+                 INIT_FP_SPECIAL(src_size, src_nbits, sendian, mant_dig, dst_size,
-                         buf, saved, nelmts);
++                 INIT_FP_SPECIAL(src_size, src_nbits, sendian, mant_dig, dst_size, buf, saved, nelmts);
  #endif
-             } else
-@@ -3705,7 +3716,18 @@ test_conv_int_fp(const char *name, int r
-             INIT_FP_DENORM(long double, LDBL_MANT_DIG, src_size, src_nbits, sendian, dst_size,
-                     buf, saved, nelmts);
-         } else {
+             }
+             else
+@@ -3750,7 +3761,18 @@ test_conv_int_fp(const char *name, int r
+                            nelmts);
+         }
+         else {
 -            INIT_FP_SPECIAL(src_size, src_nbits, sendian, LDBL_MANT_DIG, dst_size, buf, saved, nelmts);
 +	    size_t mant_dig = LDBL_MANT_DIG;
 +	    if (mant_dig >= src_nbits) {
@@ -88,4 +88,4 @@ Index: hdf5-1.10.7/test/dt_arith.c
 +            INIT_FP_SPECIAL(src_size, src_nbits, sendian, mant_dig, dst_size, buf, saved, nelmts);
          }
  #endif
-     } else
+     }

hdf5-1.10.7.tar.bz2

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:02018fac7e5efc496d9539a303cfb41924a5dadffab05df9812096e273efa55e
-size 8957844

hdf5-1.10.8.tar.bz2

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:66ec544b195a4cb9f6ffed034fd82e52429d6112747c2996ab69853f606e546b
+size 9517067

hdf5-1.8.11-abort_unknown_host_config.patch

@@ -2,7 +2,7 @@ Index: configure
 ===================================================================
 --- configure.orig
 +++ configure
-@@ -4160,6 +4160,8 @@ done
+@@ -4286,6 +4286,8 @@ done
  if test "X$host_config" != "Xnone"; then
    CC_BASENAME="`echo $CC | cut -f1 -d' ' | xargs basename 2>/dev/null`"
    . $host_config
@@ -15,7 +15,7 @@ Index: configure.ac
 ===================================================================
 --- configure.ac.orig
 +++ configure.ac
-@@ -271,6 +271,8 @@ done
+@@ -294,6 +294,8 @@ done
  if test "X$host_config" != "Xnone"; then
    CC_BASENAME="`echo $CC | cut -f1 -d' ' | xargs basename 2>/dev/null`"
    . $host_config

hdf5-LD_LIBRARY_PATH.patch

@@ -1,8 +1,8 @@
-Index: hdf5-1.10.7/src/Makefile.in
+Index: hdf5-1.10.8/src/Makefile.in
 ===================================================================
---- hdf5-1.10.7.orig/src/Makefile.in
-+++ hdf5-1.10.7/src/Makefile.in
-@@ -1941,8 +1941,6 @@ help:
+--- hdf5-1.10.8.orig/src/Makefile.in
++++ hdf5-1.10.8/src/Makefile.in
+@@ -1990,8 +1990,6 @@ help:
  # Remove the generated .c file if errors occur unless HDF5_Make_Ignore
  # is set to ignore the error.
  H5Tinit.c: H5detect$(EXEEXT)
@@ -11,7 +11,7 @@ Index: hdf5-1.10.7/src/Makefile.in
  	$(RUNSERIAL) ./H5detect$(EXEEXT) > $@  ||                               \
  	    (test $$HDF5_Make_Ignore && echo "*** Error ignored") ||          \
  	    ($(RM) $@ ; exit 1)
-@@ -1953,8 +1951,6 @@ H5Tinit.c: H5detect$(EXEEXT)
+@@ -2002,8 +2000,6 @@ H5Tinit.c: H5detect$(EXEEXT)
  # Remove the generated .c file if errors occur unless HDF5_Make_Ignore
  # is set to ignore the error.
  H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings

hdf5-Remove-timestamps-from-binaries.patch

@@ -10,29 +10,30 @@ Signed-off-by: Egbert Eich <eich@suse.de>
 ---
  src/H5detect.c | 15 ---------------
  1 file changed, 15 deletions(-)
-Index: hdf5-1.10.7/src/H5detect.c
+Index: hdf5-1.10.8/src/H5detect.c
 ===================================================================
---- hdf5-1.10.7.orig/src/H5detect.c
-+++ hdf5-1.10.7/src/H5detect.c
-@@ -1234,21 +1234,6 @@ bit.\n";
+--- hdf5-1.10.8.orig/src/H5detect.c
++++ hdf5-1.10.8/src/H5detect.c
+@@ -1190,22 +1190,6 @@ bit.\n";
      fprintf(rawoutstream, "/* Generated automatically by H5detect -- do not edit */\n\n\n");
      HDfputs(FileHeader, rawoutstream); /*the copyright notice--see top of this file */
  
--    fprintf(rawoutstream, " *\n * Created:\t\t%s %2d, %4d\n",
--    month_name[tm->tm_mon], tm->tm_mday, 1900 + tm->tm_year);
--    if(pwd || real_name[0] || host_name[0]) {
+-    fprintf(rawoutstream, " *\n * Created:\t\t%s %2d, %4d\n", month_name[tm->tm_mon], tm->tm_mday,
+-            1900 + tm->tm_year);
+-    if (pwd || real_name[0] || host_name[0]) {
 -        fprintf(rawoutstream, " *\t\t\t");
--        if(real_name[0])
+-        if (real_name[0])
 -            fprintf(rawoutstream, "%s <", real_name);
 -#ifdef H5_HAVE_GETPWUID
--        if(pwd) HDfputs(pwd->pw_name, rawoutstream);
+-        if (pwd)
+-            HDfputs(pwd->pw_name, rawoutstream);
 -#endif
--        if(host_name[0])
+-        if (host_name[0])
 -            fprintf(rawoutstream, "@%s", host_name);
--        if(real_name[0])
+-        if (real_name[0])
 -            fprintf(rawoutstream, ">");
 -        HDfputc('\n', rawoutstream);
 -    }
      fprintf(rawoutstream, " *\n * Purpose:\t\t");
-     for(s = purpose; *s; s++) {
+     for (s = purpose; *s; s++) {
          HDfputc(*s, rawoutstream);

hdf5.changes

@@ -1,3 +1,77 @@
+-------------------------------------------------------------------
+Wed Feb 16 11:18:17 UTC 2022 - Atri Bhattacharya <badshah400@gmail.com>
+
+- Update to version 1.10.8:
+  * Added new option to control the build of High-Level tools
+  * Adds C++ Autotools configuration file for Intel
+  * Adds C++ Autotools configuration file for PGI
+  * Updates PGI C options
+  * CMake will now run the shell script tests in test/ by default
+  * Removed unused HDF5_ENABLE_HSIZET option from CMake
+  * CMake no longer builds the C++ library by default
+  * Removal of pre-VS2015 work-arounds
+  * Add CMake variable HDF5_LIB_INFIX
+  * Added a configure-time option to control certain compiler
+    warnings
+  * CMake option to build the HDF filter plugins project as an
+    external project
+  * Added a configure-time option to consider certain compiler
+    warnings
+  * Autotools and CMake target added to produce doxygen generated
+    documentation
+  * CMake option to build the HDF filter plugins project as an
+    external project
+  * Added CMake option to format source files
+  * Change how the release part of version, in major.minor.release
+    is checked
+  * H5Gcreate1() now rejects size_hint parameters larger than
+    UINT32_MAX
+  * H5Pset_fapl_log() no longer crashes when passed an invalid
+    fapl ID
+  * Fixes a segfault when H5Pset_mdc_log_options() is called
+    multiple times
+  * File locking now works on Windows
+  * H5Epush_ret() now requires a trailing semicolon
+  * Improved performance of H5Sget_select_elem_pointlist
+  * H5Fget_name_f fixed to handle correctly trailing whitespaces
+    and newly allocated buffers.
+  * Added new H5S functions.
+  * Refactored the perform tools and removed dependencies on test
+    library.
+  * h5repack added help text for user-defined filters.
+  * Doxygen documentation is available when configured and
+    generated.
+  * Fixed CVE-2018-17432
+  * Fixed a segmentation fault
+  * Detection of simple data transform function "x"
+  * Fixed CVE-2020-10810 - an invalid read and memory leak when
+    parsing
+  * Fixed CVE-2018-14460
+  * Fixed CVE-2018-11206
+  * Fixed CVE-2018-14033 (same issue as CVE-2020-10811)
+  * Remove underscores on header file guards
+  * H5FArray.java class:
+    - Convert the entire byte array into a 1-d array of the
+      desired type, rather than performing 1 conversion per row;
+    - Use the Java Arrays method copyOfRange to grab the section
+      of the array from (1) that is desired to be inserted into
+      the destination array.
+  * Corrected path searched by CMake find_package command
+  * Corrected pkg-config compile script
+  * Fixed CMake C++ compiler flags
+  * Autotools clang debug optimization level change
+  * Better support for libaec (open-source Szip library) in CMake
+  * Refactor CMake configure for Fortran
+  * Remove arbitrary warning flag groups from CMake builds
+  * Reclassify CMake messages, to allow new modes and --log-level
+    option
+  * Fixes Autotools determination of the stat struct having an
+    st_blocks field
+  * Changed how h5dump and h5ls identify long double.
+  * Fixed tools argument parsing.
+  * Updated doxygen comments with changes for release
+- Minor rebase of patches to apply cleanly.
+
 -------------------------------------------------------------------
 Fri Jan 29 22:05:44 UTC 2021 - Egbert Eich <eich@suse.com>
 

hdf5.spec

@@ -1,7 +1,7 @@
 #
 # spec file for package hdf5
 #
-# Copyright (c) 2021 SUSE LLC
+# Copyright (c) 2022 SUSE LLC
 #
 # All modifications and additions to the file contributed by third parties
 # remain the property of their copyright owners, unless otherwise agreed
@@ -34,8 +34,8 @@
 
 %define use_sz2 0
 
-%define vers 1.10.7
-%define _vers 1_10_7
+%define vers 1.10.8
+%define _vers 1_10_8
 %define short_ver 1.10
 %define src_ver %{version}
 %define pname hdf5
@@ -912,8 +912,6 @@ export HDF5_Make_Ignore=yes
 
 %files -n %{name}
 %{?with_hpc:%dir %my_bindir}
-%{my_bindir}/gif2h5
-%{my_bindir}/h52gif
 %{my_bindir}/h5clear
 %{my_bindir}/h5copy
 %{my_bindir}/h5debug
@@ -927,6 +925,7 @@ export HDF5_Make_Ignore=yes
 %if %{with mpi}
 %{my_bindir}/ph5diff
 %{my_bindir}/h5perf
+%{my_bindir}/perf
 %endif
 %{my_bindir}/h5perf_serial
 %{my_bindir}/h5redeploy
@@ -934,7 +933,6 @@ export HDF5_Make_Ignore=yes
 %{my_bindir}/h5repart
 %{my_bindir}/h5stat
 %{my_bindir}/h5unjam
-%{my_bindir}/h5watch
 %{my_bindir}/mirror_server
 %{my_bindir}/mirror_server_stop