Merge pull request #524 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_8 to hdf5_1_8

* commit '7557384b9b60c2561a2eb5b08027f59737cb49c7':
  Correct name of reference file to be copied
  HDFFV-10186 new testfile
  Correct statement order
  HDFFV-9055 add new test file
  Tools merge from develop-1.10

11 files changed, 82 insertions, 129 deletions

diff --git a/tools/misc/Makefile.am b/tools/misc/Makefile.am
index 882f8f2..91a045e 100644
--- a/tools/misc/Makefile.am
+++ b/tools/misc/Makefile.am
@@ -5,12 +5,10 @@
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
-# the files COPYING and Copyright.html.  COPYING can be found at the root
-# of the source code distribution tree; Copyright.html can be found at the
-# root level of an installed copy of the electronic HDF5 document set and
-# is linked from the top-level documents page.  It can also be found at
-# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
-# access to either file, you may request a copy from help@hdfgroup.org.
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
 ##
 ## Makefile.am
 ## Run automake to generate a Makefile.in from this file.
diff --git a/tools/misc/h5cc.in b/tools/misc/h5cc.in
index 1645855..9c4e3ca 100644
--- a/tools/misc/h5cc.in
+++ b/tools/misc/h5cc.in
@@ -6,12 +6,10 @@
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
-# the files COPYING and Copyright.html.  COPYING can be found at the root
-# of the source code distribution tree; Copyright.html can be found at the
-# root level of an installed copy of the electronic HDF5 document set and
-# is linked from the top-level documents page.  It can also be found at
-# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
-# access to either file, you may request a copy from help@hdfgroup.org.
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
 ##
 
 # This tool is adapted from the mpicc command of the MPICH Software.
diff --git a/tools/misc/h5debug.c b/tools/misc/h5debug.c
index e37bcb3..f758b1f 100644
--- a/tools/misc/h5debug.c
+++ b/tools/misc/h5debug.c
@@ -5,12 +5,10 @@
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 /*-------------------------------------------------------------------------
diff --git a/tools/misc/h5mkgrp.c b/tools/misc/h5mkgrp.c
index 4ec923a..597b6b3 100644
--- a/tools/misc/h5mkgrp.c
+++ b/tools/misc/h5mkgrp.c
@@ -5,12 +5,10 @@
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 
@@ -63,7 +61,7 @@ param_t params;             /* Command line parameter settings */
 static void
 leave(int ret)
 {
-    int curr_group;
+    size_t curr_group;
 
     if (params.fname)
         HDfree (params.fname);
@@ -180,8 +178,8 @@ parse_command_line(int argc, const char *argv[], param_t *parms)
     } /* end if */
 
     /* Allocate space for the group name pointers */
-    parms->ngroups = (argc - opt_ind);
-    parms->groups = HDmalloc(parms->ngroups * sizeof(char *));
+    parms->ngroups = (size_t)(argc - opt_ind);
+    parms->groups = (char **)HDmalloc(parms->ngroups * sizeof(char *));
 
     /* Retrieve the group names */
     curr_group = 0;
diff --git a/tools/misc/h5redeploy.in b/tools/misc/h5redeploy.in
index 6b6ef87..242459a 100644
--- a/tools/misc/h5redeploy.in
+++ b/tools/misc/h5redeploy.in
@@ -6,12 +6,10 @@
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
-# the files COPYING and Copyright.html.  COPYING can be found at the root
-# of the source code distribution tree; Copyright.html can be found at the
-# root level of an installed copy of the electronic HDF5 document set and
-# is linked from the top-level documents page.  It can also be found at
-# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
-# access to either file, you may request a copy from help@hdfgroup.org.
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
 #
 
 ## Update HDF5 compiler tools after the HDF5 software has been installed  ##
diff --git a/tools/misc/h5repart.c b/tools/misc/h5repart.c
index e44c957..911e0c6 100644
--- a/tools/misc/h5repart.c
+++ b/tools/misc/h5repart.c
@@ -5,12 +5,10 @@
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 /*
diff --git a/tools/misc/h5repart_gentest.c b/tools/misc/h5repart_gentest.c
index f7d9a73..5c1ff87 100644
--- a/tools/misc/h5repart_gentest.c
+++ b/tools/misc/h5repart_gentest.c
@@ -5,12 +5,10 @@
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 /*
@@ -27,12 +25,13 @@
 #define FAMILY_SIZE     1024
 #define FILENAME        "family_file%05d.h5"
 
+static int buf[FAMILY_NUMBER][FAMILY_SIZE];
+
 int main(void)
 {
     hid_t       file=(-1), fapl, space=(-1), dset=(-1);
     char        dname[]="dataset";
     int         i, j;
-    int         buf[FAMILY_NUMBER][FAMILY_SIZE];
     hsize_t     dims[2]={FAMILY_NUMBER, FAMILY_SIZE};
 
     /* Set property list and file name for FAMILY driver */
diff --git a/tools/misc/repart_test.c b/tools/misc/repart_test.c
index e6da779..372f46a 100644
--- a/tools/misc/repart_test.c
+++ b/tools/misc/repart_test.c
@@ -5,12 +5,10 @@
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 /*
diff --git a/tools/misc/talign.c b/tools/misc/talign.c
index 2d0a9d1..83bb92a 100644
--- a/tools/misc/talign.c
+++ b/tools/misc/talign.c
@@ -5,12 +5,10 @@
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the files COPYING and Copyright.html.  COPYING can be found at the root   *
- * of the source code distribution tree; Copyright.html can be found at the  *
- * root level of an installed copy of the electronic HDF5 document set and   *
- * is linked from the top-level documents page.  It can also be found at     *
- * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
- * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 /*
@@ -19,7 +17,7 @@
  */
 #include <string.h>
 #include <stdlib.h>
-/*#include <unistd.h>	*//* Required for unlink() */
+/*#include <unistd.h>    *//* Required for unlink() */
 
 #include "hdf5.h"
 #include "H5private.h"
@@ -37,11 +35,11 @@ const char *setname = "align";
 
 int main(void)
 {
-    hid_t fil,spc,set;
-    hid_t cs6, cmp, fix;
-    hid_t cmp1, cmp2, cmp3;
-    hid_t plist;
-    hid_t array_dt;
+    hid_t fil=-1, spc=-1, set=-1;
+    hid_t cs6=-1, cmp=-1, fix=-1;
+    hid_t cmp1=-1, cmp2=-1, cmp3=-1;
+    hid_t plist=-1;
+    hid_t array_dt=-1;
 
     hsize_t dim[2];
     hsize_t cdim[4];
@@ -49,7 +47,7 @@ int main(void)
     char string5[5];
     float fok[2] = {1234.0f, 2341.0f};
     float fnok[2] = {5678.0f, 6785.0f};
-    float *fptr;
+    float *fptr = NULL;
 
     char *data = NULL;
 
@@ -88,8 +86,7 @@ int main(void)
     H5Tinsert(cmp, "Not Ok", sizeof(fok) + sizeof(string5), array_dt);
     H5Tclose(array_dt);
 
-    fix = h5tools_get_native_type(cmp);
-
+    fix = H5Tget_native_type(cmp, H5T_DIR_DEFAULT);
     cmp1 = H5Tcreate(H5T_COMPOUND, sizeof(fok));
 
     cdim[0] = sizeof(fok) / sizeof(float);
@@ -108,7 +105,7 @@ int main(void)
     H5Tclose(array_dt);
 
     plist = H5Pcreate(H5P_DATASET_XFER);
-    if((error = H5Pset_preserve(plist, 1)) < 0) 
+    if((error = H5Pset_preserve(plist, 1)) < 0)
         goto out;
 
     /*
@@ -137,6 +134,7 @@ int main(void)
 
     H5Dread(set, fix, spc, H5S_ALL, H5P_DEFAULT, data);
     fptr = (float *)(data + H5Tget_member_offset(fix, 1));
+    H5Dclose(set);
 
 out:
     if(error < 0) {
@@ -194,7 +192,9 @@ out:
     if(data)
         HDfree(data);
     H5Sclose(spc);
+    H5Tclose(cs6);
     H5Tclose(cmp);
+    H5Tclose(fix);
     H5Tclose(cmp1);
     H5Tclose(cmp2);
     H5Tclose(cmp3);
@@ -205,35 +205,3 @@ out:
     return result;
 }
 
-/*-------------------------------------------------------------------------
- * Function: h5tools_get_native_type
- *
- * Purpose: Wrapper around H5Tget_native_type() to work around
- *  Problems with bitfields.
- *
- * Return: Success:    datatype ID
- *
- *  Failure:    FAIL
- *
- * Programmer: Quincey Koziol
- *              Tuesday, October  5, 2004
- *
- * Modifications:
- *
- *-------------------------------------------------------------------------
- */
-hid_t
-h5tools_get_native_type(hid_t type)
-{
-    hid_t p_type;
-    H5T_class_t type_class;
-
-    type_class = H5Tget_class(type);
-    if(type_class==H5T_BITFIELD)
-        p_type=H5Tcopy(type);
-    else
-        p_type = H5Tget_native_type(type,H5T_DIR_DEFAULT);
-
-    return(p_type);
-}
-
diff --git a/tools/misc/testh5mkgrp.sh.in b/tools/misc/testh5mkgrp.sh.in
index a0413e1..2d2e5f7 100644
--- a/tools/misc/testh5mkgrp.sh.in
+++ b/tools/misc/testh5mkgrp.sh.in
@@ -6,12 +6,10 @@
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
-# the files COPYING and Copyright.html.  COPYING can be found at the root
-# of the source code distribution tree; Copyright.html can be found at the
-# root level of an installed copy of the electronic HDF5 document set and
-# is linked from the top-level documents page.  It can also be found at
-# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
-# access to either file, you may request a copy from help@hdfgroup.org.
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
 #
 # Tests for the h5mkgrp tool
 #
@@ -103,7 +101,7 @@ COPY_TESTFILES_TO_TESTDIR()
                 $CP -f $tstfile $TESTDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
-                
+
                     # Comment out this to CREATE expected file
                     exit $EXIT_FAILURE
                 fi
@@ -127,7 +125,7 @@ CLEAN_TESTFILES_AND_TESTDIR()
 
 # Print a line-line message left justified in a field of 70 characters
 # beginning with the word "Testing".
-TESTING() 
+TESTING()
 {
     SPACES="                                                               "
     echo "Testing $* $SPACES" |cut -c1-70 |tr -d '\012'
@@ -139,7 +137,7 @@ TESTING()
 # Print a line-line message left justified in a field of 70 characters
 # beginning with the word "Verifying".
 #
-VERIFY_H5LS() 
+VERIFY_H5LS()
 {
     SPACES="                                                               "
     echo "Verifying h5ls file structure $* $SPACES" | cut -c1-70 | tr -d '\012'
@@ -151,7 +149,7 @@ VERIFY_H5LS()
 # Assumed arguments:
 # $* arguments for h5mkgrp.
 
-TOOLTEST() 
+TOOLTEST()
 {
     TESTING $H5MKGRP $@
     (
@@ -176,7 +174,7 @@ TOOLTEST()
 
 # Call the h5ls tool to verify the correct output data in the destination file
 #
-H5LSTEST() 
+H5LSTEST()
 {
     expect="$TESTDIR/`basename $1 .h5`.ls"
     actual="$TESTDIR/`basename $1 .h5`.out"
@@ -196,9 +194,11 @@ H5LSTEST()
     STDERR_FILTER $actual
 
    if [ ! -f $expect ]; then
-    # Create the expect file if it doesn't yet exist.
-    echo " CREATED"
-    cp $actual $expect
+      # Create the expect file if it doesn't yet exist.
+      echo " CREATED"
+      cp $actual $expect
+      echo "    Expected result (*.ls) missing"
+      nerrors="`expr $nerrors + 1`"
    elif $CMP $expect $actual; then
       echo " PASSED"
    else
@@ -220,7 +220,7 @@ H5LSTEST()
 # $1 is test file name
 # $2 is h5mkgrp options
 # $* are groups to create
-RUNTEST() 
+RUNTEST()
 {
     FILEOUT=$1
     shift
@@ -249,7 +249,7 @@ RUNTEST()
 # $1 is test expected output file
 # $2 is h5mkgrp options
 # $* are groups to create
-CMPTEST() 
+CMPTEST()
 {
     FILEOUT=$1
     expect="$TESTDIR/`basename $1 .h5`.txt"
@@ -265,11 +265,13 @@ CMPTEST()
     $RUNSERIAL $H5MKGRP_BIN $@
     ) >$actual 2>$actual_err
     cat $actual_err >> $actual
-    
+
    if [ ! -f $expect ]; then
     # Create the expect file if it doesn't yet exist.
-    echo " CREATED"
-    cp $actual $expect
+      echo " CREATED"
+      cp $actual $expect
+      echo "    Expected result (*.txt) missing"
+      nerrors="`expr $nerrors + 1`"
    elif $CMP $expect $actual; then
       echo " PASSED"
    else
@@ -307,7 +309,7 @@ RUNTEST h5mkgrp_several_v.h5 "-v" one two
 RUNTEST h5mkgrp_several_p.h5 "-p" one two
 RUNTEST h5mkgrp_several_l.h5 "-l" one two
 
-# Create various nested groups 
+# Create various nested groups
 RUNTEST h5mkgrp_nested_p.h5 "-p" /one/two
 RUNTEST h5mkgrp_nested_lp.h5 "-lp" /one/two
 RUNTEST h5mkgrp_nested_mult_p.h5 "-p" /one/two /three/four
diff --git a/tools/misc/testh5repart.sh.in b/tools/misc/testh5repart.sh.in
index fc33e0e..e33a905 100644
--- a/tools/misc/testh5repart.sh.in
+++ b/tools/misc/testh5repart.sh.in
@@ -6,12 +6,10 @@
 #
 # This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
-# the files COPYING and Copyright.html.  COPYING can be found at the root
-# of the source code distribution tree; Copyright.html can be found at the
-# root level of an installed copy of the electronic HDF5 document set and
-# is linked from the top-level documents page.  It can also be found at
-# http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
-# access to either file, you may request a copy from help@hdfgroup.org.
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
 #
 # Tests for the h5repart tool
 
@@ -80,13 +78,13 @@ OUTPUTTEST() {
 
 # Print a "SKIP" message
 SKIP() {
-	 TESTING $REPART $@
-	  echo  " -SKIP-"
+    TESTING $REPART $@
+    echo  " -SKIP-"
 }
 
 ##############################################################################
 ##############################################################################
-###			  T H E   T E S T S                                ###
+###              T H E   T E S T S                                ###
 ##############################################################################
 ##############################################################################