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.

    tools/test/misc/testh5repart.sh.in:
         Change the name of the temporary test directory from "testfiles"
         which is also used for 2 h5mkgrp test files under source control to
         "testrepart" to avoid deleting source controlled files when running
         "make check" in the source directory.

    Fix test scripts that remove source-controlled files during "make check" when run in-source.
    Fix test scripts that don't remove test files because they add files to test directories but don't remove them if the build directories are the same as the source directory.

    Fix any test source file or Makefile.am files for tests that leave data files are removed by neither "make check" nor "make distclean".

14 files changed, 47 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/TestH5Ocopy.java b/java/test/TestH5Ocopy.java
index 62dd886..cf0fb1f 100644
--- a/java/test/TestH5Ocopy.java
+++ b/java/test/TestH5Ocopy.java
@@ -239,6 +239,7 @@ public class TestH5Ocopy {
             try {H5.H5Pclose(ocp_plist_id);} catch (Exception ex) {}
             try {H5.H5Fclose(H5fid2);} catch (Exception ex) {}
         }
+        _deleteFile("copy.h5");
     }
 
     @Test
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
 
 #