Minor normalization w/ develop (#3073)

Mostly bin directory
* bin/release uses sha256
* bin/h5vers whitespace changes
* bin/genparser warning fixes + HL changes
* Add bin directory for make distclean

12 files changed, 75 insertions, 54 deletions

diff --git a/Makefile.am b/Makefile.am
index 72d4959..0f2a247 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -89,7 +89,7 @@ endif
 
 SUBDIRS = src $(TESTSERIAL_DIR) $(TESTPARALLEL_DIR) bin $(TOOLS_DIR) utils . \
           $(CXX_DIR) $(FORTRAN_DIR) $(JAVA_DIR) $(HDF5_HL_DIR)
-DIST_SUBDIRS = src test testpar tools utils . c++ fortran hl examples java
+DIST_SUBDIRS = src test testpar bin tools utils . c++ fortran hl examples java
 
 # Some files generated during configure that should be cleaned
 DISTCLEANFILES=config/stamp1 config/stamp2
diff --git a/autogen.sh b/autogen.sh
index 7c3cbcf..74c6c45 100755
--- a/autogen.sh
+++ b/autogen.sh
@@ -1,10 +1,10 @@
 #!/bin/sh
 #
-# Copyright by The HDF Group.                                              
-# All rights reserved.                                                     
-#                                                                          
-# This file is part of HDF5. The full HDF5 copyright notice, including     
-# terms governing use, modification, and redistribution, is contained in   
+# Copyright by The HDF Group.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
 # distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
diff --git a/bin/checkposix b/bin/checkposix
index 8aed831..d72a410 100755
--- a/bin/checkposix
+++ b/bin/checkposix
@@ -103,7 +103,7 @@ foreach $arg (@ARGV) {
         # Now find all function calls on this line which don't start with 'H'
         while (($name)=/\b([a-z_A-GI-Z]\w*)\s*\(/) {
             $_ = $';
-              
+
             # Ignore C statements that look sort of like function
             # calls.
             next if $name =~ /^(if|for|offsetof|return|sizeof|switch|while|void)$/;
@@ -186,7 +186,7 @@ foreach $arg (@ARGV) {
             }
 
             # TESTING (not comprehensive - just noise reduction)
-            
+
             # Test macros and functions (testhdf5.h)
             next if $name =~ /^(AddTest|TestErrPrintf|TestSummary|TestCleanup|TestShutdown)$/;
             next if $name =~ /^(CHECK|CHECK_PTR|CHECK_PTR_NULL|CHECK_PTR_EQ|CHECK_I)$/;
diff --git a/bin/chkcopyright b/bin/chkcopyright
index 83b3648..756afe8 100755
--- a/bin/chkcopyright
+++ b/bin/chkcopyright
@@ -9,7 +9,6 @@
 # distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
-#
 
 # Check Copyright notice.
 # Check that all the files have the proper copyright notice.
@@ -39,6 +38,7 @@ NFIXFAILEDFILES=0	# Number of files fix failed.
 NUMBEGINLINES=60	# Copyright notice should be located within the
 			# this number of lines at the beginning of the file.
 THGCOPYRIGHTSTR="Copyright by The HDF Group."
+UICOPYRIGHTSTR="Copyright by the Board of Trustees of the University of Illinois"
 
 PASSEDLOG=/tmp/h5chkright_passed.$$
 SKIPPEDLOG=/tmp/h5chkright_skipped.$$
@@ -113,10 +113,10 @@ BUILDCOPYRIGHT()
  *                                                                           *
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
- * the COPYING file, which can be found at the root of the source code
- * distribution tree, or in https://www.hdfgroup.org/licenses.
- * 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://www.hdfgroup.org/licenses.               *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
 EOF
 
     # Fortran9X source Copyright notice
@@ -126,10 +126,10 @@ EOF
 !                                                                             *
 !   This file is part of HDF5.  The full HDF5 copyright notice, including     *
 !   terms governing use, modification, and redistribution, is contained in    *
-!   the COPYING file, which can be found at the root of the source code
-!   distribution tree, or in https://www.hdfgroup.org/licenses.
-!   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://www.hdfgroup.org/licenses.               *
+!   If you do not have access to either file, you may request a copy from     *
+!   help@hdfgroup.org.                                                        *
 EOF
 
     # HTML file Copyright notice
@@ -139,10 +139,10 @@ EOF
   *                                                                           *
   * This file is part of HDF5.  The full HDF5 copyright notice, including     *
   * terms governing use, modification, and redistribution, is contained in    *
-  * the COPYING file, which can be found at the root of the source code
-  * distribution tree, or in https://www.hdfgroup.org/licenses.
-  * 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://www.hdfgroup.org/licenses.               *
+  * If you do not have access to either file, you may request a copy from     *
+  * help@hdfgroup.org.                                                        *
 EOF
 
     # Shell style Copyright notice
@@ -341,7 +341,7 @@ FindLineInFile()
 # $1 file which contains the expected copyright notice.
 # $2 file in which to look for the copyright notice.
 # Copyright notice must be found within the beginning $NUMBEGINLINES of lines.
-# Hunt for the particular string $UICOPYRIGHTSTR which signifies the beginning
+# Hunt for the particular string $THGCOPYRIGHTSTR which signifies the beginning
 # of the copyright notice.
 #
 MATCH_COPYRIGHT()
@@ -356,7 +356,7 @@ MATCH_COPYRIGHT()
     nlines=`wc -l ${COPYRIGHTFILE}  | cut -f1 -d' '`
     # Find a line that contains the copyright string and its line number in
     # the file.
-    begin=`FindLineInFile "${UICOPYRIGHTSTR}" $f`
+    begin=`FindLineInFile "${THGCOPYRIGHTSTR}" $f`
     if [ "$begin" -le 0 ] ; then
 	# Not found, generate an empty dummy file
 	cp /dev/null ${EXTRACTEDFILE}
@@ -381,7 +381,7 @@ MATCH_COPYRIGHT()
 # $1 file which contains the expected copyright notice.
 # $2 file in which to look for the copyright notice.
 # Copyright notice must be found within the beginning $NUMBEGINLINES of lines.
-# Hunt for the particular string $UICOPYRIGHTSTR which signifies the beginning
+# Hunt for the particular string $THGCOPYRIGHTSTR which signifies the beginning
 # of the copyright notice.
 #
 FIX_COPYRIGHT()
@@ -404,7 +404,12 @@ FIX_COPYRIGHT()
     # the file.
     insertbegin=`FindLineInFile "${THGCOPYRIGHTSTR}" $f`
     if [ $insertbegin -gt 0 ]; then
-	insertend=`expr $insertbegin + $nlines`		# no need to -1.  See below.
+        insertUIbegin=`FindLineInFile "${UICOPYRIGHTSTR}" $f`
+            if [ $insertUIbegin -gt 0 ]; then
+	        insertend=`expr $insertbegin + $nlines + 1`
+            else
+                insertend=`expr $insertbegin + $nlines`
+            fi
     else
 	insertbegin=`FindLineInFile "${UICOPYRIGHTSTR}" $f`
 	if [ $insertbegin -gt 0 ]; then
diff --git a/bin/genparser b/bin/genparser
index bb44a91..619dbfa 100755
--- a/bin/genparser
+++ b/bin/genparser
@@ -3,7 +3,7 @@
 # Copyright by The HDF Group.
 # All rights reserved.
 #
-# This file is part of HDF5. The full HDF5 copyright notice, including
+# This file is part of HDF5.  The full HDF5 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
 # distribution tree, or in https://www.hdfgroup.org/licenses.
@@ -236,6 +236,7 @@ do
     echo '#pragma GCC diagnostic ignored "-Wsign-conversion"                ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wstrict-overflow"                ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wstrict-prototypes"              ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wimplicit-fallthrough"           ' >> tmp.out
     echo '#if !defined (__clang__)                                          ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wlarger-than="                   ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wsuggest-attribute=const"        ' >> tmp.out
diff --git a/bin/h5vers b/bin/h5vers
index a78c24d..6716794 100755
--- a/bin/h5vers
+++ b/bin/h5vers
@@ -376,7 +376,7 @@ if ($H5_JAVA) {
   my $version_string2 = sprintf("%d, %d, %d", @newver[0,1,2]);
 
   $data =~ s/\@version HDF5 .* <BR>/\@version HDF5 $version_string1 <BR>/;
-  $data =~ s/    public final static int LIB_VERSION\[\] = \{ \d*, \d*, \d* \};/    public final static int LIB_VERSION[] = \{ $version_string2 \};/;
+  $data =~ s/    public final static int LIB_VERSION\[\] = \{\d*,.\d*,.\d*\};/    public final static int LIB_VERSION[] = \{$version_string2\};/;
 
   write_file($H5_JAVA, $data);
 }
@@ -393,7 +393,7 @@ if ($TESTH5_JAVA) {
   my $version_string1 = sprintf("%d, %d, %d", @newver[0,1,2]);
   my $version_string2 = sprintf("int majnum = %d, minnum = %d, relnum = %d", @newver[0,1,2]);
 
-  $data =~ s/        int libversion\[\] = \{ .* \};/        int libversion\[\] = \{ $version_string1 \};/;
+  $data =~ s/        int libversion\[\] = \{.*\};/        int libversion\[\] = \{$version_string1\};/;
   $data =~ s/        int majnum = \d*, minnum = \d*, relnum = \d*;/        $version_string2;/;
 
   write_file($TESTH5_JAVA, $data);
diff --git a/bin/release b/bin/release
index 359d7c0..9435657 100755
--- a/bin/release
+++ b/bin/release
@@ -52,23 +52,23 @@ for compressing the resulting tar archive (if none are given then
                    information is available in the README_HPC file.
     doc         -- produce the latest doc tree in addition to the archive.
 
-An md5 checksum is produced for each archive created and stored in the md5 file.
+A sha256 checksum is produced for each archive created and stored in the sha256 file.
 
 Examples:
 
     $ bin/release -d /tmp
     /tmp/hdf5-1.8.13-RELEASE.txt
-    /tmp/hdf5-1.8.13.md5
+    /tmp/hdf5-1.8.13.sha256
     /tmp/hdf5-1.8.13.tar
 
     $ bin/release -d /tmp gzip
     /tmp/hdf5-1.8.13-RELEASE.txt
-    /tmp/hdf5-1.8.13.md5
+    /tmp/hdf5-1.8.13.sha256
     /tmp/hdf5-1.8.13.tar.gz
 
     $ bin/release -d /tmp tar gzip zip
     /tmp/hdf5-1.8.13-RELEASE.txt
-    /tmp/hdf5-1.8.13.md5
+    /tmp/hdf5-1.8.13.sha256
     /tmp/hdf5-1.8.13.tar
     /tmp/hdf5-1.8.13.tar.gz
     /tmp/hdf5-1.8.13.tar.zip
@@ -531,43 +531,43 @@ test "$verbose" && echo "   Running tar..." 1>&2
 (cd "$tmpdir" && exec tar -ch --exclude-vcs -f "$HDF5_VERS.tar" "./$HDF5_VERS" || exit 1 )
 
 # Compress
-MD5file=$HDF5_VERS.md5
-cp /dev/null $DEST/$MD5file
+SHA256=$HDF5_VERS.sha256
+cp /dev/null $DEST/$SHA256
 for comp in $methods; do
     case $comp in
         tar)
             cp -p $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.tar
-            (cd $DEST; md5sum $HDF5_VERS.tar >> $MD5file)
+            (cd $DEST; sha256sum $HDF5_VERS.tar >> $SHA256)
             ;;
         gzip)
             test "$verbose" && echo "   Running gzip..." 1>&2
             gzip -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.gz
-            (cd $DEST; md5sum $HDF5_VERS.tar.gz >> $MD5file)
+            (cd $DEST; sha256sum $HDF5_VERS.tar.gz >> $SHA256)
             ;;
         cmake-tgz)
             test "$verbose" && echo "   Creating CMake tar.gz file..." 1>&2
             tar2cmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/CMake-$HDF5_VERS.tar.gz 1>&2
-            (cd $DEST; md5sum CMake-$HDF5_VERS.tar.gz >> $MD5file)
+            (cd $DEST; sha256sum CMake-$HDF5_VERS.tar.gz >> $SHA256)
             ;;
         hpc-cmake-tgz)
             test "$verbose" && echo "   Creating HPC-CMake tar.gz file..." 1>&2
             tar2hpccmaketgz $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/HPC-CMake-$HDF5_VERS.tar.gz 1>&2
-            (cd $DEST; md5sum HPC-CMake-$HDF5_VERS.tar.gz >> $MD5file)
+            (cd $DEST; sha256sum HPC-CMake-$HDF5_VERS.tar.gz >> $SHA256)
             ;;
         bzip2)
             test "$verbose" && echo "   Running bzip2..." 1>&2
             bzip2 -9 <$tmpdir/$HDF5_VERS.tar >$DEST/$HDF5_VERS.tar.bz2
-            (cd $DEST; md5sum $HDF5_VERS.tar.bz2 >> $MD5file)
+            (cd $DEST; sha256sum $HDF5_VERS.tar.bz2 >> $SHA256)
             ;;
         zip)
             test "$verbose" && echo "   Creating zip ball..." 1>&2
             tar2zip $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/$HDF5_VERS.zip 1>&2
-            (cd $DEST; md5sum $HDF5_VERS.zip >> $MD5file)
+            (cd $DEST; sha256sum $HDF5_VERS.zip >> $SHA256)
             ;;
         cmake-zip)
             test "$verbose" && echo "   Creating CMake-zip ball..." 1>&2
             tar2cmakezip $HDF5_VERS $tmpdir/$HDF5_VERS.tar $DEST/CMake-$HDF5_VERS.zip 1>&2
-            (cd $DEST; md5sum CMake-$HDF5_VERS.zip >> $MD5file)
+            (cd $DEST; sha256sum CMake-$HDF5_VERS.zip >> $SHA256)
             ;;
         doc)
             if [ "${DOCVERSION}" = "" ]; then
diff --git a/bin/restore.sh b/bin/restore.sh
index 0597572..85ebd1c 100755
--- a/bin/restore.sh
+++ b/bin/restore.sh
@@ -1,10 +1,10 @@
 #!/bin/sh
 #
-# Copyright by The HDF Group.                                              
-# All rights reserved.                                                     
-#                                                                          
-# This file is part of HDF5. The full HDF5 copyright notice, including     
-# terms governing use, modification, and redistribution, is contained in   
+# Copyright by The HDF Group.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
 # the COPYING file, which can be found at the root of the source code
 # distribution tree, or in https://www.hdfgroup.org/licenses.
 # If you do not have access to either file, you may request a copy from
diff --git a/bin/warnhist b/bin/warnhist
index 680a0e8..fc42209 100755
--- a/bin/warnhist
+++ b/bin/warnhist
@@ -227,6 +227,9 @@ while (<>) {
     # Skip variables with the word 'warning' in them
     next if $_ =~ /_warning_/;
 
+    # Skip AMD Optimizing Compiler (aocc) lines "<#> warning(s) generated."
+    next if $_ =~ / warnings? generated\./;
+
     # "Hide" the C++ '::' symbol until we've parsed out the parts of the line
     while($_ =~ /\:\:/) {
 	$_ =~ s/\:\:/@@@@/g;
@@ -242,6 +245,18 @@ while (<>) {
     } elsif($_ =~ /^\s*[Ww]arning:.*/) {
         $name = $last_c_name;
         ($toss, $warning, $extra, $extra2) = split /\:/, $_;
+    # Check for file-scope gcc Fortran warning output
+    } elsif($_ =~ /f\d\d\d: Warning:/) {
+        # These are interspersed with the "compiling a file" output
+        # when compiling with `make -j` and thus difficult to tie to
+        # any particular file. They are due to things like inappropriate
+        # build options and don't have a line number.
+        #
+        # They start with f, as in f951
+        $name = "(generic)";
+        $line = int(rand(1000000)); # Hack to avoid counting as duplictates
+
+        ($warning) = $_ =~ /\[(.*)\]/x;
     # Check for FORTRAN warning output
     } elsif($_ =~ /^Warning:.*/) {
         $name = $last_fort_name;
diff --git a/configure.ac b/configure.ac
index 6d4f6d7..403a82b 100644
--- a/configure.ac
+++ b/configure.ac
@@ -559,7 +559,7 @@ AC_DEFINE_UNQUOTED([PAC_C_MAX_REAL_PRECISION], $PAC_C_MAX_REAL_PRECISION, [Deter
 AC_MSG_RESULT([$PAC_C_MAX_REAL_PRECISION])
 
 ## ----------------------------------------------------------------------
-## Check if they would like the Fortran interface compiled
+## Check if the Fortran interface should be enabled
 ##
 
 ## This needs to be exposed for the library info file even if Fortran is disabled.
@@ -797,7 +797,7 @@ HDF_CXX=no
 ## AC_PROG_CXX defines some macros that Automake 1.9.x uses and will
 ## miss even if c++ is not enabled.
 AC_PROG_CXX
-AC_PROG_CXXCPP    ## this is checked for when AC_HEADER_STDC is done
+AC_PROG_CXXCPP
 
 AC_MSG_CHECKING([if c++ interface enabled])
 
@@ -922,7 +922,7 @@ esac
 
 ## ----------------------------------------------------------------------
 ## Check which archiving tool to use. This needs to be done before
-## the AM_PROG_LIBTOOL macro.
+## the LT_INIT macro.
 ##
 if test -z "$AR"; then
   AC_CHECK_PROGS([AR], [ar xar], [:], [$PATH])
@@ -1169,7 +1169,7 @@ AC_SUBST([HDF5_TOOLS])
 ## Default is to build tests and tools
 HDF5_TOOLS=yes
 
-AC_MSG_CHECKING([if building tools is disabled])
+AC_MSG_CHECKING([if building tools is enabled])
 
 AC_ARG_ENABLE([tools],
               [AS_HELP_STRING([--enable-tools],
@@ -2050,10 +2050,8 @@ if test "X$THREADSAFE" = "Xyes"; then
     AC_CACHE_VAL([hdf5_cv_system_scope_threads],
       [AC_RUN_IFELSE(
         [AC_LANG_PROGRAM([
-            #if STDC_HEADERS
             #include <stdlib.h>
             #include <pthread.h>
-            #endif
         ],[
               pthread_attr_t attribute;
               int ret;
@@ -2706,8 +2704,8 @@ AC_SUBST([INTERNAL_DEBUG_OUTPUT])
 ## too specialized or have huge performance hits. These
 ## are not listed in the "all" packages list.
 ##
-## all_packages="AC,B,B2,D,F,FA,FL,FS,HL,I,O,S,ST,T,Z"
-all_packages="AC,B2,CX,D,F,HL,I,O,S,ST,T,Z"
+## all_packages="AC,B,B2,D,F,FA,FL,FS,HL,I,O,S,T,Z"
+all_packages="AC,B2,CX,D,F,HL,I,O,S,T,Z"
 
 case "X-$INTERNAL_DEBUG_OUTPUT" in
   X-yes|X-all)
diff --git a/hl/src/H5LTanalyze.c b/hl/src/H5LTanalyze.c
index ec7247d..55505c5 100644
--- a/hl/src/H5LTanalyze.c
+++ b/hl/src/H5LTanalyze.c
@@ -10,6 +10,7 @@
 #pragma GCC diagnostic ignored "-Wsign-conversion"                
 #pragma GCC diagnostic ignored "-Wstrict-overflow"                
 #pragma GCC diagnostic ignored "-Wstrict-prototypes"              
+#pragma GCC diagnostic ignored "-Wimplicit-fallthrough"
 #if !defined (__clang__)                                          
 #pragma GCC diagnostic ignored "-Wlarger-than="                   
 #pragma GCC diagnostic ignored "-Wsuggest-attribute=const"        
diff --git a/hl/src/H5LTparse.c b/hl/src/H5LTparse.c
index 7f552d8..fe9854e 100644
--- a/hl/src/H5LTparse.c
+++ b/hl/src/H5LTparse.c
@@ -10,6 +10,7 @@
 #pragma GCC diagnostic ignored "-Wsign-conversion"                
 #pragma GCC diagnostic ignored "-Wstrict-overflow"                
 #pragma GCC diagnostic ignored "-Wstrict-prototypes"              
+#pragma GCC diagnostic ignored "-Wimplicit-fallthrough"           
 #if !defined (__clang__)                                          
 #pragma GCC diagnostic ignored "-Wlarger-than="                   
 #pragma GCC diagnostic ignored "-Wsuggest-attribute=const"