VFD SWMR: sync with develop (#1825)

* bin directory sync

* doxygen changes

* C++ sync with develop

* Fortran sync with develop

* Sync various docs with develop

* Java sync with develop

* More doxygen sync with develop

* tools sync with develop

* h5test.h testing macros get enclosed in do..while loops (#1721)

* Minor examples normalization with develop

* hl sync with develop

* sprintf to snprintf (#1815)

* Misc sync w/ develop

* Brings some selection I/O bits over from develop

* Brings over some const fixes from develop

* Brings over more const bits from develop

* Minor bits missed in early syncs

* Brings over rest of selection I/O

* Sync of mirror VFD changes w/ develop

* Committing clang-format changes

* Adds missing testpar file

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

8 files changed, 54 insertions, 37 deletions

diff --git a/java/examples/datasets/JavaDatasetExample.sh.in b/java/examples/datasets/JavaDatasetExample.sh.in
index 9a5ddd8..b299ff2 100644
--- a/java/examples/datasets/JavaDatasetExample.sh.in
+++ b/java/examples/datasets/JavaDatasetExample.sh.in
@@ -29,6 +29,7 @@ CMP='cmp'
 DIFF='diff -c'
 CP='cp'
 DIRNAME='dirname'
+BASENAME='basename'
 LS='ls'
 AWK='awk'
 
@@ -103,17 +104,21 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             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
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
                     # Comment out this to CREATE expected file
                     exit $EXIT_FAILURE
                 fi
+                BNAME=`$BASENAME $tstfile`
+                if [ "$BNAME" = "libhdf5_java.dylib" ]; then
+                    COPIED_LIBHDF5_JAVA=1
+                fi
             fi
         fi
     done
-    if [ "$IS_DARWIN" = "yes" ]; then
+    if [[ "$IS_DARWIN" = "yes" ]] && [[ $COPIED_LIBHDF5_JAVA -eq 1 ]]; then
        (cd $BLDLIBDIR; \
          install_name_tool -add_rpath @loader_path libhdf5_java.dylib; \
          exist_path=` otool -l libhdf5_java.dylib | grep libhdf5 | grep -v java | awk '{print $2}'`; \
@@ -134,7 +139,7 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             INODE_SDIR=`$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
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
@@ -155,10 +160,7 @@ CLEAN_LIBFILES_AND_BLDLIBDIR()
     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
-        for tstfile in $COPY_JARTESTFILES
-        do
-            $RM $BLDLIBDIR/tstfile
-        done
+        $RM -rf $BLDLIBDIR
     fi
 }
 
diff --git a/java/examples/datatypes/JavaDatatypeExample.sh.in b/java/examples/datatypes/JavaDatatypeExample.sh.in
index c6f5dbc..a82d883 100644
--- a/java/examples/datatypes/JavaDatatypeExample.sh.in
+++ b/java/examples/datatypes/JavaDatatypeExample.sh.in
@@ -26,6 +26,7 @@ CMP='cmp'
 DIFF='diff -c'
 CP='cp'
 DIRNAME='dirname'
+BASENAME='basename'
 LS='ls'
 AWK='awk'
 
@@ -100,17 +101,21 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             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
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
                     # Comment out this to CREATE expected file
                     exit $EXIT_FAILURE
                 fi
+                BNAME=`$BASENAME $tstfile`
+                if [ "$BNAME" = "libhdf5_java.dylib" ]; then
+                    COPIED_LIBHDF5_JAVA=1
+                fi
             fi
         fi
     done
-    if [ "$IS_DARWIN" = "yes" ]; then
+    if [[ "$IS_DARWIN" = "yes" ]] && [[ $COPIED_LIBHDF5_JAVA -eq 1 ]]; then
        (cd $BLDLIBDIR; \
          install_name_tool -add_rpath @loader_path libhdf5_java.dylib; \
          exist_path=` otool -l libhdf5_java.dylib | grep libhdf5 | grep -v java | awk '{print $2}'`; \
@@ -131,7 +136,7 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             INODE_SDIR=`$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
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
@@ -152,10 +157,7 @@ CLEAN_LIBFILES_AND_BLDLIBDIR()
     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
-        for tstfile in $COPY_JARTESTFILES
-        do
-            $RM $BLDLIBDIR/tstfile
-        done
+        $RM -rf $BLDLIBDIR
     fi
 }
 
diff --git a/java/examples/groups/JavaGroupExample.sh.in b/java/examples/groups/JavaGroupExample.sh.in
index 86f90bf..1b84ed3 100644
--- a/java/examples/groups/JavaGroupExample.sh.in
+++ b/java/examples/groups/JavaGroupExample.sh.in
@@ -26,6 +26,7 @@ CMP='cmp'
 DIFF='diff -c'
 CP='cp'
 DIRNAME='dirname'
+BASENAME='basename'
 LS='ls'
 AWK='awk'
 
@@ -95,17 +96,21 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             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
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
                     # Comment out this to CREATE expected file
                     exit $EXIT_FAILURE
                 fi
+                BNAME=`$BASENAME $tstfile`
+                if [ "$BNAME" = "libhdf5_java.dylib" ]; then
+                    COPIED_LIBHDF5_JAVA=1
+                fi
             fi
         fi
     done
-    if [ "$IS_DARWIN" = "yes" ]; then
+    if [[ "$IS_DARWIN" = "yes" ]] && [[ $COPIED_LIBHDF5_JAVA -eq 1 ]]; then
        (cd $BLDLIBDIR; \
          install_name_tool -add_rpath @loader_path libhdf5_java.dylib; \
          exist_path=` otool -l libhdf5_java.dylib | grep libhdf5 | grep -v java | awk '{print $2}'`; \
@@ -126,7 +131,7 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             INODE_SDIR=`$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
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
@@ -147,10 +152,7 @@ CLEAN_LIBFILES_AND_BLDLIBDIR()
     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
-        for tstfile in $COPY_JARTESTFILES
-        do
-            $RM $BLDLIBDIR/tstfile
-        done
+        $RM -rf $BLDLIBDIR
     fi
 }
 
diff --git a/java/examples/intro/JavaIntroExample.sh.in b/java/examples/intro/JavaIntroExample.sh.in
index a095f27..41ed694 100644
--- a/java/examples/intro/JavaIntroExample.sh.in
+++ b/java/examples/intro/JavaIntroExample.sh.in
@@ -26,6 +26,7 @@ CMP='cmp'
 DIFF='diff -c'
 CP='cp'
 DIRNAME='dirname'
+BASENAME='basename'
 LS='ls'
 AWK='awk'
 
@@ -89,17 +90,21 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             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
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
                     # Comment out this to CREATE expected file
                     exit $EXIT_FAILURE
                 fi
+                BNAME=`$BASENAME $tstfile`
+                if [ "$BNAME" = "libhdf5_java.dylib" ]; then
+                    COPIED_LIBHDF5_JAVA=1
+                fi
             fi
         fi
     done
-    if [ "$IS_DARWIN" = "yes" ]; then
+    if [[ "$IS_DARWIN" = "yes" ]] && [[ $COPIED_LIBHDF5_JAVA -eq 1 ]]; then
        (cd $BLDLIBDIR; \
          install_name_tool -add_rpath @loader_path libhdf5_java.dylib; \
          exist_path=` otool -l libhdf5_java.dylib | grep libhdf5 | grep -v java | awk '{print $2}'`; \
@@ -120,7 +125,7 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             INODE_SDIR=`$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
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
@@ -141,10 +146,7 @@ CLEAN_LIBFILES_AND_BLDLIBDIR()
     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
-        for tstfile in $COPY_JARTESTFILES
-        do
-            $RM $BLDLIBDIR/tstfile
-        done
+        $RM -rf $BLDLIBDIR
     fi
 }
 
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 9fac20c..905a092 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -6991,7 +6991,7 @@ public class H5 implements java.io.Serializable {
     /**
      * H5Oflush causes all buffers associated with an object to be immediately flushed to disk without
      * removing the data from the cache. object_id can be any named object associated with an HDF5 file
-     * ncluding a dataset, a group, or a committed datatype.
+     * including a dataset, a group, or a committed datatype.
      *
      * @param object_id
      *            IN: Identifier of the object to be flushed.
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index cbdf463..b0c639c 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -916,6 +916,8 @@ public class HDF5Constants {
     /** */
     public static final int H5R_OBJ_REF_BUF_SIZE = H5R_OBJ_REF_BUF_SIZE();
     /** */
+    public static final int H5R_DSET_REG_REF_BUF_SIZE = H5R_DSET_REG_REF_BUF_SIZE();
+    /** */
     public static final int H5R_OBJECT = H5R_OBJECT();
     /** */
     public static final int H5R_OBJECT1 = H5R_OBJECT1();
@@ -2397,6 +2399,8 @@ public class HDF5Constants {
 
     private static native final int H5R_OBJ_REF_BUF_SIZE();
 
+    private static native final int H5R_DSET_REG_REF_BUF_SIZE();
+
     private static native final int H5R_OBJECT();
 
     private static native final int H5R_OBJECT1();
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index 2de5d87..7ea09c8 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -211,9 +211,9 @@ h5str_convert(JNIEnv *env, char **in_str, hid_t container, hid_t tid, void *out_
 
     /* Build default formats for long long types */
     if (!fmt_llong[0]) {
-        if (HDsnprintf(fmt_llong, sizeof(fmt_llong), "%%%sd", H5_PRINTF_LL_WIDTH) < 0)
+        if (HDsnprintf(fmt_llong, sizeof(fmt_llong), "%%lld") < 0)
             H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsnprintf failure");
-        if (HDsnprintf(fmt_ullong, sizeof(fmt_ullong), "%%%su", H5_PRINTF_LL_WIDTH) < 0)
+        if (HDsnprintf(fmt_ullong, sizeof(fmt_ullong), "%%llu") < 0)
             H5_JNI_FATAL_ERROR(ENVONLY, "h5str_convert: HDsnprintf failure");
     } /* end if */
 
@@ -781,9 +781,9 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
 
     /* Build default formats for long long types */
     if (!fmt_llong[0]) {
-        if (HDsnprintf(fmt_llong, sizeof(fmt_llong), "%%%sd", H5_PRINTF_LL_WIDTH) < 0)
+        if (HDsnprintf(fmt_llong, sizeof(fmt_llong), "%%lld") < 0)
             H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
-        if (HDsnprintf(fmt_ullong, sizeof(fmt_ullong), "%%%su", H5_PRINTF_LL_WIDTH) < 0)
+        if (HDsnprintf(fmt_ullong, sizeof(fmt_ullong), "%%llu") < 0)
             H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
     } /* end if */
     switch (tclass) {
diff --git a/java/test/junit.sh.in b/java/test/junit.sh.in
index ca2b3a9..4e5152b 100644
--- a/java/test/junit.sh.in
+++ b/java/test/junit.sh.in
@@ -31,6 +31,7 @@ CMP='cmp'
 DIFF='diff -c'
 CP='cp'
 DIRNAME='dirname'
+BASENAME='basename'
 LS='ls'
 AWK='awk'
 
@@ -141,17 +142,21 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             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
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
                     # Comment out this to CREATE expected file
                     exit $EXIT_FAILURE
                 fi
+                BNAME=`$BASENAME $tstfile`
+                if [ "$BNAME" = "libhdf5_java.dylib" ]; then
+                    COPIED_LIBHDF5_JAVA=1
+                fi
             fi
         fi
     done
-    if [ "$IS_DARWIN" = "yes" ]; then
+    if [[ "$IS_DARWIN" = "yes" ]] && [[ $COPIED_LIBHDF5_JAVA -eq 1 ]]; then
        (cd testlibs; \
          install_name_tool -add_rpath @loader_path libhdf5_java.dylib; \
          exist_path=` otool -l libhdf5_java.dylib | grep libhdf5 | grep -v java | awk '{print $2}'`; \
@@ -172,7 +177,7 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             INODE_SDIR=`$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
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
@@ -195,7 +200,7 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             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
+                $CP -fR $tstfile $BLDLIBDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."