Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)

* commit 'bd85e57904f1f943774bb99ea5e8b0d074db0edb':
  tools/test/h5diff/testh5diff.sh.in:          Add code to delete copies of test .h5 files copied from          tools/testfiles/vds to tools/test/h5diff/testfiles when running          "make check" for an in-source build.

13 files changed, 46 insertions, 6 deletions

diff --git a/c++/test/tfile.cpp b/c++/test/tfile.cpp
index c7ed933..f1844b6 100644
--- a/c++/test/tfile.cpp
+++ b/c++/test/tfile.cpp
@@ -846,7 +846,7 @@ void cleanup_file()
     HDremove(FILE1.c_str());
     HDremove(FILE2.c_str());
     HDremove(FILE3.c_str());
-//    HDremove(FILE4.c_str());
+    HDremove(FILE4.c_str());
     HDremove(FILE5.c_str());
     HDremove(FILE6.c_str());
 }   // cleanup_file
diff --git a/fortran/src/Makefile.am b/fortran/src/Makefile.am
index a271666..51775db 100644
--- a/fortran/src/Makefile.am
+++ b/fortran/src/Makefile.am
@@ -57,9 +57,9 @@ libhdf5_fortran_la_LIBADD=$(LIBHDF5)
 # Remove it only when distclean.
 DISTCLEANFILES=h5fc
 
-# H5fortran_types.F90 and H5f90i.h are automatically generaed by
+# H5fortran_types.F90 and H5f90i.h are automatically generated by
 # H5match_types, and must be cleaned explicitly.
-MOSTLYCLEANFILES=H5fortran_types.F90 H5f90i_gen.h
+MOSTLYCLEANFILES=H5fortran_types.F90 H5f90i_gen.h H5_gen.F90
 
 # Fortran module files can have different extensions and different names
 # (e.g., different capitalizations) on different platforms.  Write rules
diff --git a/java/examples/datasets/runExample.sh.in b/java/examples/datasets/runExample.sh.in
index 440de33..53d8070 100644
--- a/java/examples/datasets/runExample.sh.in
+++ b/java/examples/datasets/runExample.sh.in
@@ -161,6 +161,8 @@ CLEAN_DATAFILES_AND_BLDDIR()
 {
         $RM $BLDDIR/examples.datasets.H5Ex_D_*.txt
         $RM $BLDDIR/H5Ex_D_*.out
+        $RM $BLDDIR/H5Ex_D_*.h5
+        $RM $BLDDIR/H5Ex_D_External.data
 }
 
 # Print a line-line message left justified in a field of 70 characters
diff --git a/java/examples/datatypes/runExample.sh.in b/java/examples/datatypes/runExample.sh.in
index 1b02774..5b8816c 100644
--- a/java/examples/datatypes/runExample.sh.in
+++ b/java/examples/datatypes/runExample.sh.in
@@ -158,6 +158,7 @@ CLEAN_DATAFILES_AND_BLDDIR()
 {
         $RM $BLDDIR/examples.datatypes.H5Ex_T_*.txt
         $RM $BLDDIR/H5Ex_T_*.out
+        $RM $BLDDIR/H5Ex_T_*.h5
 }
 
 # Print a line-line message left justified in a field of 70 characters
diff --git a/java/examples/groups/runExample.sh.in b/java/examples/groups/runExample.sh.in
index 665b307..2a3f1c6 100644
--- a/java/examples/groups/runExample.sh.in
+++ b/java/examples/groups/runExample.sh.in
@@ -153,6 +153,14 @@ CLEAN_DATAFILES_AND_BLDDIR()
 {
         $RM $BLDDIR/examples.groups.H5Ex_G_*.txt
         $RM $BLDDIR/H5Ex_G_*.out
+        $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 $1}'`
+        if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then            SDIR=`$DIRNAME $tstfile`
+            $RM $BLDDIR/h5ex_g_iterate.h5
+            $RM $BLDDIR/h5ex_g_visit.h5
+        fi  
 }
 
 COPY_REFFILES="$LIST_REF_FILES"
diff --git a/java/examples/intro/runExample.sh.in b/java/examples/intro/runExample.sh.in
index a8e65ff..65ca160 100644
--- a/java/examples/intro/runExample.sh.in
+++ b/java/examples/intro/runExample.sh.in
@@ -147,6 +147,7 @@ CLEAN_DATAFILES_AND_BLDDIR()
 {
         $RM $BLDDIR/examples.intro.H5_*.txt
         $RM $BLDDIR/H5_*.out
+        $RM $BLDDIR/H5_*.h5
 }
 
 # Print a line-line message left justified in a field of 70 characters
diff --git a/java/src/Makefile.am b/java/src/Makefile.am
index 21aa5ec..d9e6f50 100644
--- a/java/src/Makefile.am
+++ b/java/src/Makefile.am
@@ -130,6 +130,7 @@ CLEANFILES = classhdf5_java.stamp $(jarfile) $(JAVAROOT)/$(pkgpath)/callbacks/*.
 clean:
 	rm -rf $(JAVAROOT)/*
 	rm -f $(jarfile)
+	rm -rf javadoc
 	rm -f classhdf5_java.stamp
 
 
diff --git a/java/test/junit.sh.in b/java/test/junit.sh.in
index a9a71cb..31037ba 100644
--- a/java/test/junit.sh.in
+++ b/java/test/junit.sh.in
@@ -183,7 +183,16 @@ CLEAN_DATAFILES_AND_BLDDIR()
         $RM $BLDDIR/JUnit-interface.out
         $RM $BLDDIR/JUnit-interface.err
         $RM $BLDDIR/JUnit-interface.ext
+    # skip rm if srcdir is same as destdir
+    # this occurs when build/test performed in source dir and
+    # make cp fail
+    SDIR=`$DIRNAME $tstfile`
+    INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
+    INODE_DDIR=`$LS -i -d $BLDDIR | $AWK -F' ' '{print $1}'`
+    if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
+        $RM $BLDDIR/JUnit-interface.ert
         $RM $BLDDIR/JUnit-interface.txt
+    fi        
 }
 
 # Print a line-line message left justified in a field of 70 characters
diff --git a/test/Makefile.am b/test/Makefile.am
index 37883c4..50b2ee2 100644
--- a/test/Makefile.am
+++ b/test/Makefile.am
@@ -174,7 +174,7 @@ CHECK_CLEANFILES+=accum.h5 cmpd_dset.h5 compact_dataset.h5 dataset.h5 dset_offse
     flushrefresh_VERIFICATION_CHECKPOINT1 flushrefresh_VERIFICATION_CHECKPOINT2 \
     flushrefresh_VERIFICATION_DONE accum_swmr_big.h5 ohdr_swmr.h5 \
     cache_logging.h5 cache_logging.out \
-    swmr[0-2].h5
+    swmr[0-2].h5 tbogus.h5.copy
 # Sources for testhdf5 executable
 testhdf5_SOURCES=testhdf5.c tarray.c tattr.c tchecksum.c tconfig.c tfile.c \
     tgenprop.c th5o.c th5s.c tcoords.c theap.c tid.c titerate.c tmeta.c tmisc.c \
diff --git a/tools/test/h5diff/testh5diff.sh.in b/tools/test/h5diff/testh5diff.sh.in
index d2f1397..39b87ca 100644
--- a/tools/test/h5diff/testh5diff.sh.in
+++ b/tools/test/h5diff/testh5diff.sh.in
@@ -382,6 +382,21 @@ CLEAN_TESTFILES_AND_TESTDIR()
     INODE_DDIR=`$LS -i -d $TESTDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
         $RM $TESTDIR
+    else
+        # files in $LIST_HDF5_VDS_TEST_FILES are copied in from a different
+        # directory, so when srcdir is the same as destdir and $TESTDIR is
+        # not deleted, the copy n $TESTDIR of each file from
+        # $LIST_HDF5_VDS_TEST_FILES will need to be deleted.
+        for tstfile in $LIST_HDF5_VDS_TEST_FILES
+        do
+            # ignore '#' comment
+            echo $tstfile | tr -d ' ' | grep '^#' > /dev/null
+            RET=$?
+            if [ $RET -eq 1 ]; then
+                fname=`basename $tstfile`
+                rm $TESTDIR/$fname
+            fi
+        done
     fi
 }
 
diff --git a/tools/test/h5format_convert/testh5fc.sh.in b/tools/test/h5format_convert/testh5fc.sh.in
index 5384354..24f04d6 100644
--- a/tools/test/h5format_convert/testh5fc.sh.in
+++ b/tools/test/h5format_convert/testh5fc.sh.in
@@ -180,6 +180,9 @@ CLEAN_TESTFILES_AND_TESTDIR()
         $RM $TESTDIR
     else
 	$RM $TESTDIR/$TMPFILE
+        $RM $TESTDIR/$TMPOUTFILE
+        $RM $TESTDIR/$TMPCHKFILE
+        $RM $TESTDIR/$TMPDMPFILE
     fi
 }
 
diff --git a/tools/test/misc/Makefile.am b/tools/test/misc/Makefile.am
index 1025a8a..fc9e1c1 100644
--- a/tools/test/misc/Makefile.am
+++ b/tools/test/misc/Makefile.am
@@ -36,7 +36,7 @@ SCRIPT_DEPEND=../../src/misc/h5repart$(EXEEXT) ../../src/misc/h5mkgrp$(EXEEXT) .
 # Temporary files.  *.h5 are generated by h5repart_gentest.  They should
 # copied to the testfiles/ directory if update is required. fst_family*.h5
 # and scd_family*.h5 were created by setting the HDF5_NOCLEANUP variable.
-CHECK_CLEANFILES+=*.h5 ../testfiles/fst_family*.h5 ../testfiles/scd_family*.h5
+CHECK_CLEANFILES+=*.h5 ../testfiles/fst_family*.h5 ../testfiles/scd_family*.h5 append.log
 
 # These were generated by configure.  Remove them only when distclean.
 DISTCLEANFILES=testh5repart.sh testh5clear.sh
diff --git a/tools/test/misc/testh5repart.sh.in b/tools/test/misc/testh5repart.sh.in
index 2106a1d..9a9dd9a 100644
--- a/tools/test/misc/testh5repart.sh.in
+++ b/tools/test/misc/testh5repart.sh.in
@@ -43,7 +43,7 @@ SRC_TOOLS="$srcdir/../.."
 
 SRC_TOOLS_TESTFILES="$SRC_TOOLS/testfiles"
 
-TESTDIR=./testfiles
+TESTDIR=./testrepart
 test -d $TESTDIR || mkdir -p $TESTDIR
 
 #