Merge pull request #1296 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:1.10/master to 1.10/master

* commit 'f3f29dc7df5f3cc41a5e9462d8c415e540cda3d6': (42 commits)
  Commit version string changes for HDF5 1.10.4 release.
  Merge hdf5_1_10 changes to hdf5_1_10_4.
  Merge in changes from hdf5_1_10.
  Commit release date change.
  Update RELEASE.txt for HDF5 1.10.4 release.
  Add notes about unsupported options
  Add contents of HDF5 1.10.3 RELEASE.txt to HISTORY-1_10.txt and update RELEASE.txt for continuing development.
  Switch maintainer mode to disable, build mode to production, version to 1.10.4, and commit files generated by autogen.sh for release branch hdf5_1_10_4.
  HDFFV-10568 fix hdf5_java library dependency
  Fix Java library location for testing
  Java groups example fix
  Update system commands with HD prefix and whitespace
  Merge pull request #1224 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to develop
  Disable failing tests because of execution issue
  Add testfiles to data copy
  Same changes needed for examples as test
  Correct name of test jar
  Only remove test jars
  Remove obsolete var
  Change prefix in example scripts to relative path to bin. This was done for 1.8, and works wherever installed without the need to replace the original prefix.
  ...

4 files changed, 151 insertions, 50 deletions

diff --git a/java/examples/datasets/JavaDatasetExample.sh.in b/java/examples/datasets/JavaDatasetExample.sh.in
index cb16d45..f5c63cd 100644
--- a/java/examples/datasets/JavaDatasetExample.sh.in
+++ b/java/examples/datasets/JavaDatasetExample.sh.in
@@ -52,12 +52,14 @@ test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
 #       Comment '#' without space can be used.
 # --------------------------------------------------------------------
 LIST_LIBRARY_FILES="
-$HDFLIB_HOME/slf4j-api-1.7.25.jar
-$HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar
 $top_builddir/src/.libs/libhdf5.*
 $top_builddir/java/src/jni/.libs/libhdf5_java.*
 $top_builddir/java/src/$JARFILE
 "
+LIST_JAR_TESTFILES="
+$HDFLIB_HOME/slf4j-api-1.7.25.jar
+$HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar
+"
 LIST_DATA_FILES="
 $HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Alloc.txt
 $HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Checksum.txt
@@ -83,6 +85,7 @@ $HDFTEST_HOME/../testfiles/examples.datasets.H5Ex_D_Soint.txt
 # copy files from source dirs to test dir
 #
 COPY_LIBFILES="$LIST_LIBRARY_FILES"
+COPY_JARTESTFILES="$LIST_JAR_TESTFILES"
 
 COPY_LIBFILES_TO_BLDLIBDIR()
 {
@@ -110,6 +113,30 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             fi
         fi
     done
+    # copy jar files. Used -f to make sure get a new copy
+    for tstfile in $COPY_JARTESTFILES
+    do
+        # ignore '#' comment
+        echo $tstfile | tr -d ' ' | grep '^#' > /dev/null
+        RET=$?
+        if [ $RET -eq 1 ]; then
+            # skip cp if srcdir is same as destdir
+            # this occurs when build/test performed in source dir and
+            # make cp fail
+            SDIR=`$DIRNAME $tstfile`
+            INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
+            INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
+            if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
+                $CP -f $tstfile $BLDLIBDIR
+                if [ $? -ne 0 ]; then
+                    echo "Error: FAILED to copy $tstfile ."
+
+                    # Comment out this to CREATE expected file
+                    exit $EXIT_FAILURE
+                fi
+            fi
+        fi
+    done
 }
 
 CLEAN_LIBFILES_AND_BLDLIBDIR()
@@ -117,11 +144,14 @@ CLEAN_LIBFILES_AND_BLDLIBDIR()
     # skip rm if srcdir is same as destdir
     # this occurs when build/test performed in source dir and
     # make cp fail
-    SDIR=`$DIRNAME $HDFLIB_HOME/slf4j-api-1.7.25.jar`
+    SDIR=$HDFLIB_HOME
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
     INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-        $RM $BLDLIBDIR
+        for tstfile in $COPY_JARTESTFILES
+        do
+            $RM $BLDLIBDIR/tstfile
+        done
     fi
 }
 
@@ -215,14 +245,9 @@ if $TEST -z "$LD_LIBRARY_PATH" ; then
 fi
 
 case  $os_name in
-    Darwin)
-    DYLD_LIBRARY_PATH=$BLDLIBDIR:$DYLD_LIBRARY_PATH
-    export DYLD_LIBRARY_PATH
-    LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH
-    ;;
     *)
     LD_LIBRARY_PATH=$BLDLIBDIR:$LD_LIBRARY_PATH
-        ;;
+    ;;
 esac
 
 export LD_LIBRARY_PATH
diff --git a/java/examples/datatypes/JavaDatatypeExample.sh.in b/java/examples/datatypes/JavaDatatypeExample.sh.in
index 033442a..447512a 100644
--- a/java/examples/datatypes/JavaDatatypeExample.sh.in
+++ b/java/examples/datatypes/JavaDatatypeExample.sh.in
@@ -49,12 +49,14 @@ test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
 #       Comment '#' without space can be used.
 # --------------------------------------------------------------------
 LIST_LIBRARY_FILES="
-$HDFLIB_HOME/slf4j-api-1.7.25.jar
-$HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar
 $top_builddir/src/.libs/libhdf5.*
 $top_builddir/java/src/jni/.libs/libhdf5_java.*
 $top_builddir/java/src/$JARFILE
 "
+LIST_JAR_TESTFILES="
+$HDFLIB_HOME/slf4j-api-1.7.25.jar
+$HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar
+"
 LIST_DATA_FILES="
 $HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_Array.txt
 $HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_ArrayAttribute.txt
@@ -80,6 +82,7 @@ $HDFTEST_HOME/../testfiles/examples.datatypes.H5Ex_T_VLString.txt
 # copy files from source dirs to test dir
 #
 COPY_LIBFILES="$LIST_LIBRARY_FILES"
+COPY_JARTESTFILES="$LIST_JAR_TESTFILES"
 
 COPY_LIBFILES_TO_BLDLIBDIR()
 {
@@ -107,6 +110,30 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             fi
         fi
     done
+    # copy jar files. Used -f to make sure get a new copy
+    for tstfile in $COPY_JARTESTFILES
+    do
+        # ignore '#' comment
+        echo $tstfile | tr -d ' ' | grep '^#' > /dev/null
+        RET=$?
+        if [ $RET -eq 1 ]; then
+            # skip cp if srcdir is same as destdir
+            # this occurs when build/test performed in source dir and
+            # make cp fail
+            SDIR=`$DIRNAME $tstfile`
+            INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
+            INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
+            if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
+                $CP -f $tstfile $BLDLIBDIR
+                if [ $? -ne 0 ]; then
+                    echo "Error: FAILED to copy $tstfile ."
+
+                    # Comment out this to CREATE expected file
+                    exit $EXIT_FAILURE
+                fi
+            fi
+        fi
+    done
 }
 
 CLEAN_LIBFILES_AND_BLDLIBDIR()
@@ -114,11 +141,14 @@ CLEAN_LIBFILES_AND_BLDLIBDIR()
     # skip rm if srcdir is same as destdir
     # this occurs when build/test performed in source dir and
     # make cp fail
-    SDIR=`$DIRNAME $HDFLIB_HOME/slf4j-api-1.7.25.jar`
+    SDIR=$HDFLIB_HOME
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
     INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-        $RM $BLDLIBDIR
+        for tstfile in $COPY_JARTESTFILES
+        do
+            $RM $BLDLIBDIR/tstfile
+        done
     fi
 }
 
@@ -211,11 +241,6 @@ if $TEST -z "$LD_LIBRARY_PATH" ; then
 fi
 
 case  $os_name in
-    Darwin)
-    DYLD_LIBRARY_PATH=$BLDLIBDIR:$DYLD_LIBRARY_PATH
-    export DYLD_LIBRARY_PATH
-    LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH
-    ;;
     *)
     LD_LIBRARY_PATH=$BLDLIBDIR:$LD_LIBRARY_PATH
     ;;
diff --git a/java/examples/groups/JavaGroupExample.sh.in b/java/examples/groups/JavaGroupExample.sh.in
index 36df02e..9d4673f 100644
--- a/java/examples/groups/JavaGroupExample.sh.in
+++ b/java/examples/groups/JavaGroupExample.sh.in
@@ -34,13 +34,13 @@ nerrors=0
 # where the libs exist
 HDFLIB_HOME="$top_srcdir/java/lib"
 BLDLIBDIR="$top_builddir/hdf5/lib"
-BLDREFDIR="./groups"
+BLDITERDIR="./groups"
 BLDDIR="."
 HDFTEST_HOME="$top_srcdir/java/examples/groups"
 JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
 TESTJARFILE=jar@PACKAGE_TARNAME@groups.jar
 test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
-test -d $BLDREFDIR || mkdir -p $BLDREFDIR
+test -d $BLDITERDIR || mkdir -p $BLDITERDIR
 
 ######################################################################
 # library files
@@ -51,13 +51,15 @@ test -d $BLDREFDIR || mkdir -p $BLDREFDIR
 #       Comment '#' without space can be used.
 # --------------------------------------------------------------------
 LIST_LIBRARY_FILES="
-$HDFLIB_HOME/slf4j-api-1.7.25.jar
-$HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar
 $top_builddir/src/.libs/libhdf5.*
 $top_builddir/java/src/jni/.libs/libhdf5_java.*
 $top_builddir/java/src/$JARFILE
 "
-LIST_REF_FILES="
+LIST_JAR_TESTFILES="
+$HDFLIB_HOME/slf4j-api-1.7.25.jar
+$HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar
+"
+LIST_ITER_FILES="
 $HDFTEST_HOME/h5ex_g_iterate.h5
 $HDFTEST_HOME/h5ex_g_visit.h5
 "
@@ -75,6 +77,7 @@ $HDFTEST_HOME/../testfiles/examples.groups.H5Ex_G_Visit.txt
 # copy files from source dirs to test dir
 #
 COPY_LIBFILES="$LIST_LIBRARY_FILES"
+COPY_JARTESTFILES="$LIST_JAR_TESTFILES"
 
 COPY_LIBFILES_TO_BLDLIBDIR()
 {
@@ -102,6 +105,30 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             fi
         fi
     done
+    # copy jar files. Used -f to make sure get a new copy
+    for tstfile in $COPY_JARTESTFILES
+    do
+        # ignore '#' comment
+        echo $tstfile | tr -d ' ' | grep '^#' > /dev/null
+        RET=$?
+        if [ $RET -eq 1 ]; then
+            # skip cp if srcdir is same as destdir
+            # this occurs when build/test performed in source dir and
+            # make cp fail
+            SDIR=`$DIRNAME $tstfile`
+            INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
+            INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
+            if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
+                $CP -f $tstfile $BLDLIBDIR
+                if [ $? -ne 0 ]; then
+                    echo "Error: FAILED to copy $tstfile ."
+
+                    # Comment out this to CREATE expected file
+                    exit $EXIT_FAILURE
+                fi
+            fi
+        fi
+    done
 }
 
 CLEAN_LIBFILES_AND_BLDLIBDIR()
@@ -109,11 +136,14 @@ CLEAN_LIBFILES_AND_BLDLIBDIR()
     # skip rm if srcdir is same as destdir
     # this occurs when build/test performed in source dir and
     # make cp fail
-    SDIR=`$DIRNAME $HDFLIB_HOME/slf4j-api-1.7.25.jar`
+    SDIR=$HDFLIB_HOME
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
     INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-        $RM $BLDLIBDIR
+        for tstfile in $COPY_JARTESTFILES
+        do
+            $RM $BLDLIBDIR/tstfile
+        done
     fi
 }
 
@@ -152,6 +182,7 @@ CLEAN_DATAFILES_AND_BLDDIR()
         $RM $BLDDIR/examples.groups.H5Ex_G_*.txt
         $RM $BLDDIR/H5Ex_G_*.out
         $RM $BLDDIR/H5Ex_G_*.h5
+        $RM $BLDDIR/h5ex_g_*.h5
         SDIR=`$DIRNAME $tstfile`
         INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
         INODE_DDIR=`$LS -i -d $BLDDIR | $AWK -F' ' '{print $1}'`
@@ -161,12 +192,12 @@ CLEAN_DATAFILES_AND_BLDDIR()
         fi
 }
 
-COPY_REFFILES="$LIST_REF_FILES"
+COPY_ITERFILES="$LIST_ITER_FILES"
 
-COPY_REFFILES_TO_BLDREFDIR()
+COPY_ITERFILES_TO_BLDITERDIR()
 {
     # copy test files. Used -f to make sure get a new copy
-    for tstfile in $COPY_REFFILES
+    for tstfile in $COPY_ITERFILES
     do
         # ignore '#' comment
         echo $tstfile | tr -d ' ' | grep '^#' > /dev/null
@@ -177,9 +208,9 @@ COPY_REFFILES_TO_BLDREFDIR()
             # make cp fail
             SDIR=`$DIRNAME $tstfile`
             INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
-            INODE_DDIR=`$LS -i -d $BLDREFDIR | $AWK -F' ' '{print $1}'`
+            INODE_DDIR=`$LS -i -d $BLDITERDIR | $AWK -F' ' '{print $1}'`
             if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-                $CP -f $tstfile $BLDREFDIR
+                $CP -f $tstfile $BLDITERDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
@@ -191,16 +222,16 @@ COPY_REFFILES_TO_BLDREFDIR()
     done
 }
 
-CLEAN_REFFILES_AND_BLDREFDIR()
+CLEAN_ITERFILES_AND_BLDITERDIR()
 {
     # skip rm if srcdir is same as destdir
     # this occurs when build/test performed in source dir and
     # make cp fail
     SDIR=`$DIRNAME $HDFTEST_HOME/h5ex_g_iterate.h5`
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
-    INODE_DDIR=`$LS -i -d $BLDREFDIR | $AWK -F' ' '{print $1}'`
+    INODE_DDIR=`$LS -i -d $BLDITERDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-        $RM $BLDREFDIR
+        $RM $BLDITERDIR
     fi
 }
 
@@ -223,7 +254,7 @@ JAVAEXEFLAGS=@H5_JAVAFLAGS@
 # prepare for test
 COPY_LIBFILES_TO_BLDLIBDIR
 COPY_DATAFILES_TO_BLDDIR
-COPY_REFFILES_TO_BLDREFDIR
+COPY_ITERFILES_TO_BLDITERDIR
 
 CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.25.jar:"$BLDLIBDIR"/slf4j-simple-1.7.25.jar:"$TESTJARFILE""
 
@@ -257,11 +288,6 @@ if $TEST -z "$LD_LIBRARY_PATH" ; then
 fi
 
 case  $os_name in
-    Darwin)
-    DYLD_LIBRARY_PATH=$BLDLIBDIR:$DYLD_LIBRARY_PATH
-    export DYLD_LIBRARY_PATH
-    LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH
-    ;;
     *)
     LD_LIBRARY_PATH=$BLDLIBDIR:$LD_LIBRARY_PATH
     ;;
@@ -340,9 +366,9 @@ else
 fi
 
 # Clean up temporary files/directories
+CLEAN_ITERFILES_AND_BLDITERDIR
 CLEAN_LIBFILES_AND_BLDLIBDIR
 CLEAN_DATAFILES_AND_BLDDIR
-CLEAN_REFFILES_AND_BLDREFDIR
 
 # Report test results and exit
 if test $nerrors -eq 0 ; then
diff --git a/java/examples/intro/JavaIntroExample.sh.in b/java/examples/intro/JavaIntroExample.sh.in
index 077146d..1886485 100644
--- a/java/examples/intro/JavaIntroExample.sh.in
+++ b/java/examples/intro/JavaIntroExample.sh.in
@@ -49,12 +49,14 @@ test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
 #       Comment '#' without space can be used.
 # --------------------------------------------------------------------
 LIST_LIBRARY_FILES="
-$HDFLIB_HOME/slf4j-api-1.7.25.jar
-$HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar
 $top_builddir/src/.libs/libhdf5.*
 $top_builddir/java/src/jni/.libs/libhdf5_java.*
 $top_builddir/java/src/$JARFILE
 "
+LIST_JAR_TESTFILES="
+$HDFLIB_HOME/slf4j-api-1.7.25.jar
+$HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar
+"
 LIST_DATA_FILES="
 $HDFTEST_HOME/../testfiles/examples.intro.H5_CreateDataset.txt
 $HDFTEST_HOME/../testfiles/examples.intro.H5_CreateAttribute.txt
@@ -69,6 +71,7 @@ $HDFTEST_HOME/../testfiles/examples.intro.H5_ReadWrite.txt
 # copy files from source dirs to test dir
 #
 COPY_LIBFILES="$LIST_LIBRARY_FILES"
+COPY_JARTESTFILES="$LIST_JAR_TESTFILES"
 
 COPY_LIBFILES_TO_BLDLIBDIR()
 {
@@ -96,6 +99,30 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             fi
         fi
     done
+    # copy jar files. Used -f to make sure get a new copy
+    for tstfile in $COPY_JARTESTFILES
+    do
+        # ignore '#' comment
+        echo $tstfile | tr -d ' ' | grep '^#' > /dev/null
+        RET=$?
+        if [ $RET -eq 1 ]; then
+            # skip cp if srcdir is same as destdir
+            # this occurs when build/test performed in source dir and
+            # make cp fail
+            SDIR=`$DIRNAME $tstfile`
+            INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
+            INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
+            if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
+                $CP -f $tstfile $BLDLIBDIR
+                if [ $? -ne 0 ]; then
+                    echo "Error: FAILED to copy $tstfile ."
+
+                    # Comment out this to CREATE expected file
+                    exit $EXIT_FAILURE
+                fi
+            fi
+        fi
+    done
 }
 
 CLEAN_LIBFILES_AND_BLDLIBDIR()
@@ -103,11 +130,14 @@ CLEAN_LIBFILES_AND_BLDLIBDIR()
     # skip rm if srcdir is same as destdir
     # this occurs when build/test performed in source dir and
     # make cp fail
-    SDIR=`$DIRNAME $HDFLIB_HOME/slf4j-api-1.7.25.jar`
+    SDIR=$HDFLIB_HOME
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
     INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-        $RM $BLDLIBDIR
+        for tstfile in $COPY_JARTESTFILES
+        do
+            $RM $BLDLIBDIR/tstfile
+        done
     fi
 }
 
@@ -200,11 +230,6 @@ if $TEST -z "$LD_LIBRARY_PATH" ; then
 fi
 
 case  $os_name in
-    Darwin)
-    DYLD_LIBRARY_PATH=$BLDLIBDIR:$DYLD_LIBRARY_PATH
-    export DYLD_LIBRARY_PATH
-    LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH
-    ;;
     *)
     LD_LIBRARY_PATH=$BLDLIBDIR:$LD_LIBRARY_PATH
     ;;