Merge branch 'develop' into feature/new_datatypes

CMakeLists.txt

@@ -919,8 +919,8 @@ if (HDF5_ENABLE_THREADSAFE)
       message (VERBOSE " **** Allowing unsupported HL and thread-safety options **** ")
     endif ()
   endif ()
-  if (H5_HAVE_IOEO)
-    message (VERBOSE " **** Win32 threads requires WINVER>=0x600 (Windows Vista/7/8) **** ")
+  if (WIN32)
+    # When Win32 is available, we use those threads
     set (H5_HAVE_WIN_THREADS 1)
   else ()
     if (NOT H5_HAVE_PTHREAD_H)

HDF5Examples/C/H5T/h5ex_t_array.c

@@ -144,7 +144,7 @@ main(void)
      * Output the data to the screen.
      */
     for (i = 0; i < dims[0]; i++) {
-        printf("%s[%llu]:\n", DATASET, i);
+        printf("%s[%" PRIuHSIZE "]:\n", DATASET, i);
         for (j = 0; j < adims[0]; j++) {
             printf(" [");
             for (k = 0; k < adims[1]; k++)

HDF5Examples/C/H5T/h5ex_t_arrayatt.c

@@ -155,7 +155,7 @@ main(void)
      * Output the data to the screen.
      */
     for (i = 0; i < dims[0]; i++) {
-        printf("%s[%llu]:\n", ATTRIBUTE, i);
+        printf("%s[%" PRIuHSIZE "]:\n", ATTRIBUTE, i);
         for (j = 0; j < adims[0]; j++) {
             printf(" [");
             for (k = 0; k < adims[1]; k++)

HDF5Examples/C/H5T/h5ex_t_cmpd.c

@@ -136,7 +136,7 @@ main(void)
      * Output the data to the screen.
      */
     for (i = 0; i < dims[0]; i++) {
-        printf("%s[%llu]:\n", DATASET, i);
+        printf("%s[%" PRIuHSIZE "]:\n", DATASET, i);
         printf("Serial number   : %d\n", rdata[i].serial_no);
         printf("Location        : %s\n", rdata[i].location);
         printf("Temperature (F) : %f\n", rdata[i].temperature);

HDF5Examples/C/H5T/h5ex_t_cmpdatt.c

@@ -146,7 +146,7 @@ main(void)
      * Output the data to the screen.
      */
     for (i = 0; i < dims[0]; i++) {
-        printf("%s[%llu]:\n", ATTRIBUTE, i);
+        printf("%s[%" PRIuHSIZE "]:\n", ATTRIBUTE, i);
         printf("Serial number   : %d\n", rdata[i].serial_no);
         printf("Location        : %s\n", rdata[i].location);
         printf("Temperature (F) : %f\n", rdata[i].temperature);

HDF5Examples/C/H5T/h5ex_t_cpxcmpd.c

@@ -293,7 +293,7 @@ main(void)
      * Output the data to the screen.
      */
     for (i = 0; i < dims[0]; i++) {
-        printf("%s[%llu]:\n", DATASET, i);
+        printf("%s[%" PRIuHSIZE "]:\n", DATASET, i);
         printf("   Vehicle name :\n      %s\n", rdata[i].name);
         printf("   Sensor locations :\n");
         for (j = 0; j < rdata[i].sensors.len; j++)

HDF5Examples/C/H5T/h5ex_t_cpxcmpdatt.c

@@ -304,7 +304,7 @@ main(void)
      * Output the data to the screen.
      */
     for (i = 0; i < dims[0]; i++) {
-        printf("%s[%llu]:\n", ATTRIBUTE, i);
+        printf("%s[%" PRIuHSIZE "]:\n", ATTRIBUTE, i);
         printf("   Vehicle name :\n      %s\n", rdata[i].name);
         printf("   Sensor locations :\n");
         for (j = 0; j < rdata[i].sensors.len; j++)

HDF5Examples/C/H5T/h5ex_t_objref.c

@@ -135,7 +135,7 @@ main(void)
      * Output the data to the screen.
      */
     for (i = 0; i < dims[0]; i++) {
-        printf("%s[%llu]:\n  ->", DATASET, i);
+        printf("%s[%" PRIuHSIZE "]:\n  ->", DATASET, i);
 
         /*
          * Open the referenced object, get its name and type.
@@ -174,6 +174,9 @@ main(void)
             case H5O_TYPE_NAMED_DATATYPE:
                 printf("Named Datatype");
                 break;
+            case H5O_TYPE_MAP:
+                printf("Map Object");
+                break;
             case H5O_TYPE_UNKNOWN:
             case H5O_TYPE_NTYPES:
                 printf("Unknown");

HDF5Examples/C/H5T/h5ex_t_objrefatt.c

@@ -147,7 +147,7 @@ main(void)
      * Output the data to the screen.
      */
     for (i = 0; i < dims[0]; i++) {
-        printf("%s[%llu]:\n  ->", ATTRIBUTE, i);
+        printf("%s[%" PRIuHSIZE "]:\n  ->", ATTRIBUTE, i);
 
         /*
          * Open the referenced object, get its name and type.
@@ -186,6 +186,9 @@ main(void)
             case H5O_TYPE_NAMED_DATATYPE:
                 printf("Named Datatype");
                 break;
+            case H5O_TYPE_MAP:
+                printf("Map Object");
+                break;
             case H5O_TYPE_UNKNOWN:
             case H5O_TYPE_NTYPES:
                 printf("Unknown");

HDF5Examples/C/H5T/h5ex_t_opaqueatt.c

@@ -121,7 +121,7 @@ main(void)
      */
     printf("Datatype tag for %s is: \"%s\"\n", ATTRIBUTE, tag);
     for (i = 0; i < dims[0]; i++) {
-        printf("%s[%llu]: ", ATTRIBUTE, i);
+        printf("%s[%" PRIuHSIZE "]: ", ATTRIBUTE, i);
         for (j = 0; j < len; j++)
             printf("%c", rdata[j + i * len]);
         printf("\n");

HDF5Examples/C/H5T/h5ex_t_regref.c

@@ -168,7 +168,7 @@ main(void)
      * Output the data to the screen.
      */
     for (i = 0; i < dims[0]; i++) {
-        printf("%s[%llu]:\n  ->", DATASET, i);
+        printf("%s[%" PRIuHSIZE "]:\n  ->", DATASET, i);
 
         /*
          * Open the referenced object, retrieve its region as a

HDF5Examples/C/H5T/h5ex_t_regrefatt.c

@@ -183,7 +183,7 @@ main(void)
      * Output the data to the screen.
      */
     for (i = 0; i < dims[0]; i++) {
-        printf("%s[%llu]:\n  ->", ATTRIBUTE, i);
+        printf("%s[%" PRIuHSIZE "]:\n  ->", ATTRIBUTE, i);
 
         /*
          * Open the referenced object, retrieve its region as a

HDF5Examples/C/H5T/h5ex_t_vlen.c

@@ -118,7 +118,7 @@ main(void)
      * Output the variable-length data to the screen.
      */
     for (i = 0; i < dims[0]; i++) {
-        printf("%s[%llu]:\n  {", DATASET, i);
+        printf("%s[%" PRIuHSIZE "]:\n  {", DATASET, i);
         ptr = rdata[i].p;
         for (j = 0; j < rdata[i].len; j++) {
             printf(" %d", ptr[j]);

HDF5Examples/C/H5T/h5ex_t_vlenatt.c

@@ -128,7 +128,7 @@ main(void)
      * Output the variable-length data to the screen.
      */
     for (i = 0; i < dims[0]; i++) {
-        printf("%s[%llu]:\n  {", ATTRIBUTE, i);
+        printf("%s[%" PRIuHSIZE "]:\n  {", ATTRIBUTE, i);
         ptr = rdata[i].p;
         for (j = 0; j < rdata[i].len; j++) {
             printf(" %d", ptr[j]);

config/cmake/ConfigureChecks.cmake

@@ -143,7 +143,6 @@ else ()
 endif ()
 
 if (CYGWIN)
-  set (${HDF_PREFIX}_HAVE_LSEEK64 0)
   set (CMAKE_REQUIRED_DEFINITIONS "${CMAKE_REQUIRED_DEFINITIONS} -D_GNU_SOURCE")
   add_definitions ("-D_GNU_SOURCE")
 endif ()
@@ -262,6 +261,13 @@ endif ()
 #
 # https://docs.oracle.com/cd/E23824_01/html/821-1474/lfcompile-5.html
 
+# MinGW and Cygwin
+if (MINGW OR CYGWIN)
+  set (CMAKE_REQUIRED_DEFINITIONS
+    "${CURRENT_TEST_DEFINITIONS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE"
+  )
+endif ()
+
 #-----------------------------------------------------------------------------
 #  Check the size in bytes of all the int and float types
 #-----------------------------------------------------------------------------
@@ -327,7 +333,7 @@ if (MINGW OR NOT WINDOWS)
 endif ()
 
 HDF_CHECK_TYPE_SIZE (off_t          ${HDF_PREFIX}_SIZEOF_OFF_T)
-HDF_CHECK_TYPE_SIZE (time_t          ${HDF_PREFIX}_SIZEOF_TIME_T)
+HDF_CHECK_TYPE_SIZE (time_t         ${HDF_PREFIX}_SIZEOF_TIME_T)
 
 #-----------------------------------------------------------------------------
 # Extra C99 types
@@ -440,62 +446,6 @@ if (MINGW OR NOT WINDOWS)
   endforeach ()
 endif ()
 
-#-----------------------------------------------------------------------------
-# Check if InitOnceExecuteOnce is available
-#-----------------------------------------------------------------------------
-if (WINDOWS)
-  if (NOT HDF_NO_IOEO_TEST)
-    message (VERBOSE "Checking for InitOnceExecuteOnce:")
-  if (NOT DEFINED ${HDF_PREFIX}_HAVE_IOEO)
-    if (LARGEFILE)
-      set (CMAKE_REQUIRED_DEFINITIONS
-          "${CURRENT_TEST_DEFINITIONS} -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE"
-      )
-    endif ()
-    set (MACRO_CHECK_FUNCTION_DEFINITIONS "-DHAVE_IOEO ${CMAKE_REQUIRED_FLAGS}")
-    if (CMAKE_REQUIRED_INCLUDES)
-      set (CHECK_C_SOURCE_COMPILES_ADD_INCLUDES "-DINCLUDE_DIRECTORIES:STRING=${CMAKE_REQUIRED_INCLUDES}")
-    else ()
-      set (CHECK_C_SOURCE_COMPILES_ADD_INCLUDES)
-    endif ()
-
-    TRY_RUN(HAVE_IOEO_EXITCODE HAVE_IOEO_COMPILED
-        ${CMAKE_BINARY_DIR}
-        ${HDF_RESOURCES_DIR}/HDFTests.c
-        COMPILE_DEFINITIONS "${CMAKE_REQUIRED_DEFINITIONS} ${MACRO_CHECK_FUNCTION_DEFINITIONS}"
-        LINK_LIBRARIES "${HDF5_REQUIRED_LIBRARIES}"
-        CMAKE_FLAGS "${CHECK_C_SOURCE_COMPILES_ADD_INCLUDES} -DCMAKE_SKIP_RPATH:BOOL=${CMAKE_SKIP_RPATH}"
-        COMPILE_OUTPUT_VARIABLE OUTPUT
-    )
-    # if it did not compile make the return value fail code of 1
-    if (NOT HAVE_IOEO_COMPILED)
-      set (HAVE_IOEO_EXITCODE 1)
-    endif ()
-    # if the return value was 0 then it worked
-    if ("${HAVE_IOEO_EXITCODE}" EQUAL 0)
-      set (${HDF_PREFIX}_HAVE_IOEO 1 CACHE INTERNAL "Test InitOnceExecuteOnce")
-      message (VERBOSE "Performing Test InitOnceExecuteOnce - Success")
-      file (APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeOutput.log
-        "Performing C SOURCE FILE Test InitOnceExecuteOnce succeeded with the following output:\n"
-        "${OUTPUT}\n"
-        "Return value: ${HAVE_IOEO}\n")
-    else ()
-      if (CMAKE_CROSSCOMPILING AND "${HAVE_IOEO_EXITCODE}" MATCHES  "FAILED_TO_RUN")
-        set (${HDF_PREFIX}_HAVE_IOEO "${HAVE_IOEO_EXITCODE}")
-      else ()
-        set (${HDF_PREFIX}_HAVE_IOEO "" CACHE INTERNAL "Test InitOnceExecuteOnce")
-      endif ()
-
-      message (VERBOSE "Performing Test InitOnceExecuteOnce - Failed")
-      file (APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log
-        "Performing InitOnceExecuteOnce Test  failed with the following output:\n"
-        "${OUTPUT}\n"
-        "Return value: ${HAVE_IOEO_EXITCODE}\n")
-    endif ()
-  endif ()
-  endif ()
-endif ()
-
 # ----------------------------------------------------------------------
 # Set the flag to indicate that the machine can handle converting
 # denormalized floating-point values.

config/cmake/H5pubconf.h.in

@@ -222,9 +222,6 @@
 /* Define to 1 if you have the `z' library (-lz). */
 #cmakedefine H5_HAVE_LIBZ @H5_HAVE_LIBZ@
 
-/* Define to 1 if you have the `lseek64' function. */
-#cmakedefine H5_HAVE_LSEEK64 @H5_HAVE_LSEEK64@
-
 /* Define if the map API (H5M) should be compiled */
 #cmakedefine H5_HAVE_MAP_API @H5_HAVE_MAP_API@
 
@@ -289,9 +286,6 @@
    compiled */
 #cmakedefine H5_HAVE_ROS3_VFD @H5_HAVE_ROS3_VFD@
 
-/* Define to 1 if you have the `stat64' function. */
-#cmakedefine H5_HAVE_STAT64 @H5_HAVE_STAT64@
-
 /* Define if struct stat has the st_blocks field */
 #cmakedefine H5_HAVE_STAT_ST_BLOCKS @H5_HAVE_STAT_ST_BLOCKS@
 

config/cmake/HDFTests.c

@@ -126,21 +126,3 @@ main(void)
 #endif
 }
 #endif
-
-#ifdef HAVE_IOEO
-
-#include <windows.h>
-typedef void (WINAPI *PGNSI)(LPSYSTEM_INFO);
-int main ()
-{
-    PGNSI pGNSI;
-
-    pGNSI = (PGNSI) GetProcAddress(GetModuleHandle(TEXT("kernel32.dll")), "InitOnceExecuteOnce");
-
-    if (NULL == pGNSI)
-        return 1;
-    else
-        return 0;
-}
-
-#endif /* HAVE_IOEO */

doxygen/aliases

@@ -235,7 +235,6 @@ ALIASES += sa_metadata_ops="\sa \li H5Pget_all_coll_metadata_ops() \li H5Pget_co
 ################################################################################
 
 ALIASES += ref_cons_semantics="<a href=\"https://portal.hdfgroup.org/display/HDF5/Enabling+a+Strict+Consistency+Semantics+Model+in+Parallel+HDF5\">Enabling a Strict Consistency Semantics Model in Parallel HDF5</a>"
-ALIASES += ref_dld_filters="<a href=\"https://portal.hdfgroup.org/display/HDF5/HDF5+Dynamically+Loaded+Filters\">HDF5 Dynamically Loaded Filters</a>"
 ALIASES += ref_file_image_ops="<a href=\"https://portal.hdfgroup.org/display/HDF5/HDF5+File+Image+Operations\">HDF5 File Image Operations</a>"
 ALIASES += ref_filter_pipe="<a href=\"https://portal.hdfgroup.org/display/HDF5/HDF5+Data+Flow+Pipeline+for+H5Dread\">Data Flow Pipeline for H5Dread()</a>"
 ALIASES += ref_group_impls="<a href=\"https://portal.hdfgroup.org/display/HDF5/Groups\">Group implementations in HDF5</a>"

doxygen/dox/UsersGuide.dox

@@ -134,6 +134,7 @@ HDF5 Release 1.14
         <li> \ref subsubsec_dataset_transfer_props
         <li> \ref subsubsec_dataset_transfer_store
         <li> \ref subsubsec_dataset_transfer_partial
+        <li> \ref subsubsec_dataset_transfer_dyn_filter
     </ul>
 \li \ref subsec_dataset_allocation
     <ul>
@@ -147,6 +148,7 @@ HDF5 Release 1.14
         <li> \ref subsubsec_dataset_filters_nbit
         <li> \ref subsubsec_dataset_filters_scale
         <li> \ref subsubsec_dataset_filters_szip
+        <li> \ref subsubsec_dataset_filters_dyn
     </ul>
 
 \ref sec_datatype

doxygen/examples/H5.format.1.1.html

@@ -5436,8 +5436,8 @@ <h4><a name="FilterMessage">Name: Data Storage - Filter Pipeline</a></h4>
             filters requested and supported by third parties.
             Filters supported by The HDF Group are documented immediately
             below.  Information on 3rd-party filters can be found at
-            <a href="/services/contributions.html#filters">
-            <code>https://support.hdfgroup.org/services/contributions.html#filters</code></a>.
+            <a href="https://portal.hdfgroup.org/documentation/hdf5-docs/registered_filter_plugins.html">
+            <code>https://portal.hdfgroup.org/documentation/hdf5-docs/registered_filter_plugins.html</code></a>.
             <a href="#Footnote1Change"><sup><small>1</small></sup></a>
             <p>
             To request a filter identifier, please contact

doxygen/examples/H5.format.2.0.html

@@ -12598,9 +12598,8 @@ <h4>
                     HDF5 Library and for filters requested and supported by third
                     parties. Filters supported by The HDF Group are documented
                     immediately below. Information on 3rd-party filters can be found at
-                    The HDF Group&rsquo;s <a
-                        href="http://www.hdfgroup.org/services/contributions.html">
-                        Contributions</a> page.
+                    The HDF Group&rsquo;s <a href="https://portal.hdfgroup.org/documentation/hdf5-docs/registered_filter_plugins.html">
+                    Registered Filters</a> page.
                 </p>
 
                 <p>
@@ -12854,9 +12853,8 @@ <h4>
                     HDF5 Library and for filters requested and supported by third
                     parties. Filters supported by The HDF Group are documented
                     immediately below. Information on 3rd-party filters can be found at
-                    The HDF Group&rsquo;s <a
-                        href="http://www.hdfgroup.org/services/contributions.html">
-                        Contributions</a> page.
+                    The HDF Group&rsquo;s <a href="https://portal.hdfgroup.org/documentation/hdf5-docs/registered_filter_plugins.html">
+                    Registered Filters</a> page.
                 </p>
 
                 <p>

doxygen/examples/H5.format.html

@@ -14226,8 +14226,8 @@ <h4><a name="FilterMessage">IV.A.2.l. The Data Storage - Filter
           Filters supported by The HDF Group are documented immediately
           below.  Information on 3rd-party filters can be found at
           The HDF Group&rsquo;s
-          <a href="http://www.hdfgroup.org/services/contributions.html">
-            Contributions</a> page.</p>
+          <a href="https://portal.hdfgroup.org/documentation/hdf5-docs/registered_filter_plugins.html">
+          Registered Filters</a> page.</p>
 
         <p>
           To request a filter identifier, please contact
@@ -14488,8 +14488,8 @@ <h4><a name="FilterMessage">IV.A.2.l. The Data Storage - Filter
           Filters supported by The HDF Group are documented immediately
           below.  Information on 3rd-party filters can be found at
           The HDF Group&rsquo;s
-          <a href="http://www.hdfgroup.org/services/contributions.html">
-            Contributions</a> page.</p>
+          <a href="https://portal.hdfgroup.org/documentation/hdf5-docs/registered_filter_plugins.html">
+          Registered Filters</a> page.</p>
 
         <p>
           To request a filter identifier, please contact

java/src/jni/h5pImp.c

@@ -563,8 +563,8 @@ Java_hdf_hdf5lib_H5_H5Pisa_1class(JNIEnv *env, jclass clss, jlong plid, jlong pc
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_H5_H5Pget(JNIEnv *env, jclass clss, jlong plid, jstring name)
 {
-    const char *cstr = NULL;
-    jint        val;
+    const char *cstr   = NULL;
+    jint        val    = -1;
     herr_t      status = FAIL;
 
     UNUSED(clss);

m4/aclocal_fc.m4

@@ -159,7 +159,7 @@ dnl disable Fortran 2003 if it does not.
 
 AC_DEFUN([PAC_PROG_FC_HAVE_F2003_REQUIREMENTS],[
    HAVE_F2003_REQUIREMENTS="no"
-   AC_MSG_CHECKING([if Fortran compiler version compatible with Fortran 2003 HDF])
+   AC_MSG_CHECKING([if Fortran compiler version compatible with Fortran 2003])
    TEST_SRC="`sed -n '/PROG_FC_HAVE_F2003_REQUIREMENTS/,/END PROGRAM PROG_FC_HAVE_F2003_REQUIREMENTS/p' $srcdir/m4/aclocal_fc.f90`"
    AC_COMPILE_IFELSE([$TEST_SRC], [AC_MSG_RESULT([yes])
             HAVE_F2003_REQUIREMENTS="yes"],