Merge remote-tracking branch 'origin/develop' into ts_h5fl_reg

.codespellrc

@@ -1,6 +1,6 @@
 # Ref: https://github.com/codespell-project/codespell#using-a-config-file
 [codespell]
-skip = .git,*.svg,.codespellrc,./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c,./config/sanitizer/LICENSE,./config/sanitizer/sanitizers.cmake,./tools/test/h5import/testfiles/*.conf,./tools/test/h5repack/testfiles/*.dat,./test/API/driver,./configure,./bin/ltmain.sh,./bin/depcomp,./bin/config.guess,./bin/config.sub,./autom4te.cache,./m4/libtool.m4,./c++/src/*.html,./HDF5Examples/depcomp
+skip = .git,*.svg,.codespellrc,./bin/trace,./hl/tools/h5watch/h5watch.c,./tools/test/h5jam/tellub.c,./config/sanitizer/LICENSE,./config/sanitizer/sanitizers.cmake,./tools/test/h5import/testfiles/*.conf,./tools/test/h5repack/testfiles/*.dat,./test/API/driver,./configure,./bin/ltmain.sh,./bin/depcomp,./bin/config.guess,./bin/config.sub,./autom4te.cache,./m4/libtool.m4,./c++/src/*.html,./HDF5Examples/depcomp,./release_docs/HISTORY-*.txt
 check-hidden = true
 # ignore-regex = 
-ignore-words-list = ot,isnt,inout,nd,parms,parm,ba,offsetP,ser,ois,had,fiter,fo,clude,refere,minnum,offsetp,creat,ans:,eiter,lastr,ans,isn't,ifset,sur,trun,dne,tthe,hda,filname,te,htmp,ake,gord,numer,ro,oce,msdos,TEXTIN,FLE
+ignore-words-list = ot,isnt,inout,nd,parms,parm,ba,offsetP,ser,ois,had,fiter,fo,clude,refere,minnum,offsetp,creat,ans:,eiter,lastr,ans,isn't,ifset,sur,trun,dne,tthe,hda,filname,te,htmp,ake,gord,numer,ro,oce,msdos,TEXTIN,indx,FLE

.devcontainer/Dockerfile

@@ -2,4 +2,4 @@ FROM mcr.microsoft.com/devcontainers/base:debian
 
 RUN apt-get update && apt-get -y install --no-install-recommends \
   build-essential cmake cmake-curses-gui doxygen git graphviz \
-  less libtool-bin libyajl-dev mpi-default-dev valgrind wget
+  less libtool-bin libyajl-dev mpi-default-dev ninja-build valgrind wget

HDF5Examples/C/H5FLT/tfiles/h5ex_d_bshuf.ddl

@@ -11,7 +11,7 @@ GROUP "/" {
          USER_DEFINED_FILTER {
             FILTER_ID 32008
             COMMENT bitshuffle; see https://github.com/kiyo-masui/bitshuffle
-            PARAMS { 0 3 4 0 0 0 }
+            PARAMS { 0 4 4 0 0 0 }
          }
       }
       FILLVALUE {

c++/src/H5DataType.cpp

@@ -250,7 +250,7 @@ DataType::p_decode() const
     }
 
     // Call C function to decode the binary object description
-    hid_t encoded_dtype_id = H5Tdecode(encoded_buf);
+    hid_t encoded_dtype_id = H5Tdecode2(encoded_buf, buf_size);
 
     // If H5Tdecode fails, raise exception
     if (encoded_dtype_id < 0) {
@@ -924,7 +924,8 @@ DataType::close()
         // Free and reset buffer of encoded object description if it's been used
         if (encoded_buf != NULL) {
             delete[] encoded_buf;
-            buf_size = 0;
+            encoded_buf = NULL;
+            buf_size    = 0;
         }
     }
 }

config/cmake/cacheinit.cmake

@@ -94,7 +94,7 @@ set (BSHUF_GIT_URL "https://github.com/kiyo-masui/bitshuffle.git" CACHE STRING "
 set (BSHUF_GIT_BRANCH "master" CACHE STRING "" FORCE)
 
 set (BSHUF_TGZ_ORIGPATH "https://github.com/kiyo-masui/bitshuffle/archive/refs/tags" CACHE STRING "Use PLUGINS from original location" FORCE)
-set (BSHUF_TGZ_NAME "bitshuffle-0.5.1.tar.gz" CACHE STRING "Use BSHUF from compressed file" FORCE)
+set (BSHUF_TGZ_NAME "bitshuffle-0.5.2.tar.gz" CACHE STRING "Use BSHUF from compressed file" FORCE)
 
 set (BSHUF_PACKAGE_NAME "bshuf" CACHE STRING "Name of BSHUF package" FORCE)
 
@@ -126,7 +126,7 @@ set (BLOSC2_GIT_URL "https://github.com/Blosc/c-blosc2.git" CACHE STRING "Use BL
 set (BLOSC2_GIT_BRANCH "main" CACHE STRING "" FORCE)
 
 set (BLOSC2_TGZ_ORIGPATH "https://github.com/Blosc/c-blosc2/archive/refs/tags" CACHE STRING "Use PLUGINS from original location" FORCE)
-set (BLOSC2_TGZ_NAME "c-blosc2-2.15.1.tar.gz" CACHE STRING "Use BLOSC2 from compressed file" FORCE)
+set (BLOSC2_TGZ_NAME "c-blosc2-2.15.2.tar.gz" CACHE STRING "Use BLOSC2 from compressed file" FORCE)
 
 set (BLOSC2_PACKAGE_NAME "blosc2" CACHE STRING "Name of BLOSC2 package" FORCE)
 

doxygen/dox/ImageSpec.dox

@@ -430,7 +430,7 @@ and blue components that make up each color.
 <table>
 <tr>
 <td>
-\image html Palettes.fm.anc.gif
+\image html Palettes_fm_anc.gif
 </td>
 </tr>
 </table>

fortran/src/H5Tf.c

@@ -1890,47 +1890,6 @@ h5tcommitted_c(hid_t_f *dtype_id)
     return ret_value;
 }
 
-/****if* H5Tf/h5tdecode_c
- * NAME
- *  h5tdecode_c
- * PURPOSE
- *  Call H5Tdecode
- * INPUTS
- *
- *		buf     - Buffer for the data space object to be decoded.
- * OUTPUTS
- *
- *  obj_id  - Object_id (non-negative)
- *
- * RETURNS
- *  0 on success, -1 on failure
- * SOURCE
- */
-
-int_f
-h5tdecode_c(_fcd buf, hid_t_f *obj_id)
-/******/
-{
-    int            ret_value = -1;
-    unsigned char *c_buf     = NULL; /* Buffer to hold C string */
-    hid_t          c_obj_id;
-
-    /*
-     * Call H5Tdecode function.
-     */
-
-    c_buf = (unsigned char *)buf;
-
-    c_obj_id = H5Tdecode(c_buf);
-    if (c_obj_id < 0)
-        return ret_value;
-
-    *obj_id   = (hid_t_f)c_obj_id;
-    ret_value = 0;
-
-    return ret_value;
-}
-
 /****if* H5Tf/h5tencode_c
  * NAME
  *  h5tencode_c

fortran/src/H5Tff.F90

@@ -1855,32 +1855,47 @@ END SUBROUTINE h5tcommitted_f
 !>
 !! \ingroup FH5T
 !!
-!! \brief Decode A binary object description of data type and return a new object handle.
+!! \brief Decode a binary object description of data type and return a new object handle.
 !!
-!! \param buf    Buffer for the data space object to be decoded.
-!! \param obj_id Object ID.
-!! \param hdferr \fortran_error
+!! \param buf      Buffer for the data space object to be decoded.
+!! \param obj_id   Object ID.
+!! \param hdferr   \fortran_error
+!! \param buf_size Size of the buffer.
 !!
-!! See C API: @ref H5Tdecode()
+!! See C API: @ref H5Tdecode2()
 !!
-  SUBROUTINE h5tdecode_f(buf, obj_id, hdferr)
+SUBROUTINE h5tdecode_f(buf, obj_id, hdferr, buf_size)
     IMPLICIT NONE
     CHARACTER(LEN=*), INTENT(IN) :: buf
     INTEGER(HID_T), INTENT(OUT) :: obj_id
     INTEGER, INTENT(OUT) :: hdferr
+    INTEGER(SIZE_T), OPTIONAL, INTENT(IN) :: buf_size
+
+    INTEGER(SIZE_T) :: buf_size_default
+
     INTERFACE
-       INTEGER FUNCTION h5tdecode_c(buf, obj_id) BIND(C,NAME='h5tdecode_c')
+       INTEGER(HID_T) FUNCTION H5Tdecode2(buf, buf_size) BIND(C,NAME='H5Tdecode2')
          IMPORT :: C_CHAR
-         IMPORT :: HID_T
+         IMPORT :: HID_T, SIZE_T
          IMPLICIT NONE
-         CHARACTER(KIND=C_CHAR), DIMENSION(*), INTENT(IN) :: buf
-         INTEGER(HID_T), INTENT(OUT) :: obj_id
-       END FUNCTION h5tdecode_c
+         CHARACTER(KIND=C_CHAR), DIMENSION(*) :: buf
+         INTEGER(SIZE_T), VALUE :: buf_size
+       END FUNCTION H5Tdecode2
     END INTERFACE
 
-    hdferr = h5tdecode_c(buf, obj_id)
+    IF(PRESENT(buf_size))THEN
+        buf_size_default = buf_size
+    ELSE
+        buf_size_default = LEN(buf)
+    ENDIF
+
+    obj_id = H5Tdecode2(buf, buf_size_default)
+
+    IF(obj_id.LT.0)THEN
+      hdferr = -1
+    ENDIF
 
-  END SUBROUTINE h5tdecode_f
+END SUBROUTINE h5tdecode_f
 
 !>
 !! \ingroup FH5T

fortran/src/H5f90proto.h

@@ -327,7 +327,6 @@ H5_FCDLL int_f h5tvlen_create_c(hid_t_f *type_id, hid_t_f *vltype_id);
 H5_FCDLL int_f h5tis_variable_str_c(hid_t_f *type_id, int_f *flag);
 H5_FCDLL int_f h5tget_member_class_c(hid_t_f *type_id, int_f *member_no, int_f *cls);
 H5_FCDLL int_f h5tcommit_anon_c(hid_t_f *loc_id, hid_t_f *dtype_id, hid_t_f *tcpl_id, hid_t_f *tapl_id);
-H5_FCDLL int_f h5tdecode_c(_fcd buf, hid_t_f *obj_id);
 H5_FCDLL int_f h5tencode_c(_fcd buf, hid_t_f *obj_id, size_t_f *nalloc);
 H5_FCDLL int_f h5tget_create_plist_c(hid_t_f *dtype_id, hid_t_f *dtpl_id);
 H5_FCDLL int_f h5tcompiler_conv_c(hid_t_f *src_id, hid_t_f *dst_id, int_f *c_flag);

fortran/test/tH5T.F90

@@ -109,6 +109,7 @@ SUBROUTINE compoundtest(cleanup, total_error)
      CHARACTER(LEN=1024) :: cmpd_buf
      INTEGER(SIZE_T) :: cmpd_buf_size=0
      INTEGER(HID_T) :: decoded_tid1
+     INTEGER(HID_T) :: decoded_tid2
 
      INTEGER(HID_T) :: fixed_str1, fixed_str2
      LOGICAL :: are_equal
@@ -553,7 +554,10 @@ SUBROUTINE compoundtest(cleanup, total_error)
      CALL H5Tencode_f(dtype_id, cmpd_buf, cmpd_buf_size, error)
      CALL check("H5Tencode_f", error, total_error)
 
-     !  Try decoding bogus buffer
+     !  Try decoding bogus buffer with and without optional buffer size
+
+     CALL H5Tdecode_f(cmpd_buf, decoded_tid1, error, cmpd_buf_size)
+     CALL verify("H5Tdecode_f", error, -1, total_error)
 
      CALL H5Tdecode_f(cmpd_buf, decoded_tid1, error)
      CALL verify("H5Tdecode_f", error, -1, total_error)
@@ -562,14 +566,23 @@ SUBROUTINE compoundtest(cleanup, total_error)
      CALL check("H5Tencode_f", error, total_error)
 
      !  Decode from the compound buffer and return an object handle
-     CALL H5Tdecode_f(cmpd_buf, decoded_tid1, error)
+     CALL H5Tdecode_f(cmpd_buf, decoded_tid1, error, cmpd_buf_size)
      CALL check("H5Tdecode_f", error, total_error)
 
      !  Verify that the datatype was copied exactly
 
      CALL H5Tequal_f(decoded_tid1, dtype_id, flag, error)
      CALL check("H5Tequal_f", error, total_error)
      CALL verify("H5Tequal_f", flag, .TRUE., total_error)
+
+     ! Decode from the compound buffer without the optional parameter
+     CALL H5Tdecode_f(cmpd_buf, decoded_tid2, error)
+     CALL check("H5Tdecode_f", error, total_error)
+
+     !  Verify that the datatype was copied exactly
+     CALL H5Tequal_f(decoded_tid2, dtype_id, flag, error)
+     CALL check("H5Tequal_f", error, total_error)
+
      !
      ! Close all open objects.
      !

hl/test/test_ld.c

@@ -33,7 +33,7 @@
 #define DSET_SCALAR      "DSET_SCALAR"
 
 /* Selected compound field members for testing */
-#define VALID_FIELDS1 "field1,field2.a,field3,field4" /* TEMPORORAY */
+#define VALID_FIELDS1 "field1,field2.a,field3,field4" /* TEMPORARY */
 #define VALID_FIELDS2 "field2.b.a,field2.c,field4.b"
 
 #define INVALID_FIELDS1 "field2.k.a,field2.c,field4.k"

java/src/hdf/hdf5lib/H5.java

@@ -13865,16 +13865,19 @@ public static long H5Tcreate(int tclass, long size) throws HDF5LibraryException
      * @param buf
      *            IN: Buffer for the data type object to be decoded.
      *
+     * @param buf_size
+     *           IN: Size of the buffer.
+     *
      * @return a new object handle
      *
      * @exception HDF5LibraryException
      *            Error from the HDF5 Library.
      * @exception NullPointerException
      *            buf is null.
      **/
-    public static long H5Tdecode(byte[] buf) throws HDF5LibraryException, NullPointerException
+    public static long H5Tdecode(byte[] buf, long buf_size) throws HDF5LibraryException, NullPointerException
     {
-        long id = _H5Tdecode(buf);
+        long id = _H5Tdecode(buf, buf_size);
         if (id > 0) {
             log.trace("OPEN_IDS: H5Tdecode add {}", id);
             OPEN_IDS.add(id);
@@ -13883,7 +13886,7 @@ public static long H5Tdecode(byte[] buf) throws HDF5LibraryException, NullPointe
         return id;
     }
 
-    private synchronized static native long _H5Tdecode(byte[] buf)
+    private synchronized static native long _H5Tdecode(byte[] buf, long buf_size)
         throws HDF5LibraryException, NullPointerException;
 
     /**