Merge from develop

github updates
bin scripts updates
parser changes
remove obsolete file

5 files changed, 108 insertions, 35 deletions

diff --git a/bin/format_source b/bin/format_source
index b0b695c..1128def 100755
--- a/bin/format_source
+++ b/bin/format_source
@@ -1,6 +1,26 @@
 #!/bin/bash
+#
+# Recursively format all C & C++ sources and header files, except those in the
+# 'config' directory and generated files, such as H5LTanalyze.c, etc.
+#
+# Note that any files or directories that are excluded here should also be
+# added to the 'exclude' list in .github/workflows/clang-format-check.yml
+#
+# (Remember to update both bin/format_source and bin/format_source_patch)
+
 find . -type d \( -path ./config \) -prune \
-    -o -iname *.h -o -iname *.c -o -iname *.cpp -o -iname *.hpp \
+    -or \( \( \! \( \
+        -name H5LTanalyze.c \
+        -or -name H5LTparse.c \
+        -or -name H5LTparse.h \
+        -or -name H5Epubgen.h \
+        -or -name H5Einit.h \
+        -or -name H5Eterm.h \
+        -or -name H5Edefin.h \
+        -or -name H5version.h \
+        -or -name H5overflow.h \
+        \) \) \
+    -and \( -iname *.h -or -iname *.c -or -iname *.cpp -or -iname *.hpp \) \) \
     | xargs clang-format -style=file -i -fallback-style=none
 
-exit 0
\ No newline at end of file
+exit 0
diff --git a/bin/format_source_patch b/bin/format_source_patch
index 4c531ea..8d6be01 100755
--- a/bin/format_source_patch
+++ b/bin/format_source_patch
@@ -1,6 +1,26 @@
 #!/bin/bash
+#
+# Recursively format all C & C++ sources and header files, except those in the
+# 'config' directory and generated files, such as H5LTanalyze.c, etc.
+#
+# Note that any files or directories that are excluded here should also be
+# added to the 'exclude' list in .github/workflows/clang-format-check.yml
+#
+# (Remember to update both bin/format_source and bin/format_source_patch)
+
 find . -type d \( -path ./config \) -prune \
-    -o -iname *.h -o -iname *.c -o -iname *.cpp -o -iname *.hpp \
+    -or \( \( \! \( \
+        -name H5LTanalyze.c \
+        -or -name H5LTparse.c \
+        -or -name H5LTparse.h \
+        -or -name H5Epubgen.h \
+        -or -name H5Einit.h \
+        -or -name H5Eterm.h \
+        -or -name H5Edefin.h \
+        -or -name H5version.h \
+        -or -name H5overflow.h \
+        \) \) \
+    -and \( -iname *.h -or -iname *.c -or -iname *.cpp -or -iname *.hpp \) \) \
     | xargs clang-format -style=file -i -fallback-style=none
 
 git diff > clang_format.patch
@@ -11,4 +31,4 @@ then
     rm clang_format.patch
 fi
 
-exit 0
\ No newline at end of file
+exit 0
diff --git a/bin/genparser b/bin/genparser
index e6aee5b..ab40775 100755
--- a/bin/genparser
+++ b/bin/genparser
@@ -1,10 +1,10 @@
 #! /bin/bash
 #
-# 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://support.hdfgroup.org/ftp/HDF5/releases.
 # If you do not have access to either file, you may request a copy from
@@ -200,17 +200,20 @@ if [ "$verbose" = true ] ; then
 fi
 ${HDF5_FLEX} --nounistd -PH5LTyy -o ${path_to_hl_src}/H5LTanalyze.c ${path_to_hl_src}/H5LTanalyze.l
 
-# fix H5LTparse.c to declare H5LTyyparse return type as an hid_t
-# instead of int.  Currently the generated function H5LTyyparse is
+# fix H5LTparse.c and H5LTlparse.h to declare H5LTyyparse return type as an
+# hid_t instead of int.  Currently the generated function H5LTyyparse is
 # generated with a return value of type int, which is a mapping to the
 # flex yyparse function.  The return value in the HL library should be
-# an hid_t. 
-# I propose to not use flex to generate this function, but for now I am 
+# an hid_t.
+# I propose to not use flex to generate this function, but for now I am
 # adding a perl command to find and replace this function declaration in
 # H5LTparse.c.
 perl -0777 -pi -e 's/int yyparse/hid_t yyparse/igs' ${path_to_hl_src}/H5LTparse.c
 perl -0777 -pi -e 's/int\nyyparse/hid_t\nyyparse/igs' ${path_to_hl_src}/H5LTparse.c
 perl -0777 -pi -e 's/int H5LTyyparse/hid_t H5LTyyparse/igs' ${path_to_hl_src}/H5LTparse.c
+perl -0777 -pi -e 's/int yyparse/hid_t yyparse/igs' ${path_to_hl_src}/H5LTparse.h
+perl -0777 -pi -e 's/int\nyyparse/hid_t\nyyparse/igs' ${path_to_hl_src}/H5LTparse.h
+perl -0777 -pi -e 's/int H5LTyyparse/hid_t H5LTyyparse/igs' ${path_to_hl_src}/H5LTparse.h
 
 # Add code that disables warnings in the flex/bison-generated code.
 #
@@ -218,7 +221,8 @@ perl -0777 -pi -e 's/int H5LTyyparse/hid_t H5LTyyparse/igs' ${path_to_hl_src}/H5
 # will simply ignore them, but we want to avoid those warnings.
 for f in ${path_to_hl_src}/H5LTparse.c ${path_to_hl_src}/H5LTanalyze.c
 do
-    echo '#if defined __GNUC__ && 402 <= __GNUC__ * 100 + __GNUC_MINOR__    ' >> tmp.out
+    echo '#if defined (__GNUC__)                                            ' >> tmp.out
+    echo '#if ((__GNUC__ * 100) + __GNUC_MINOR__) >= 402                    ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wconversion"                     ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wimplicit-function-declaration"  ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wlarger-than="                   ' >> tmp.out
@@ -230,11 +234,16 @@ 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 "-Wsuggest-attribute=const"        ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wsuggest-attribute=pure"         ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wswitch-default"                 ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wunused-function"                ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wunused-macros"                  ' >> tmp.out
     echo '#pragma GCC diagnostic ignored "-Wunused-parameter"               ' >> tmp.out
+    echo '#endif                                                            ' >> tmp.out
+    echo '#if ((__GNUC__ * 100) + __GNUC_MINOR__) >= 600                    ' >> tmp.out
+    echo '#pragma GCC diagnostic ignored "-Wnull-dereference"               ' >> tmp.out
+    echo '#endif                                                            ' >> tmp.out
     echo '#elif defined __SUNPRO_CC                                         ' >> tmp.out
     echo '#pragma disable_warn                                              ' >> tmp.out
     echo '#elif defined _MSC_VER                                            ' >> tmp.out
diff --git a/bin/release b/bin/release
index a775faf..f087ae8 100755
--- a/bin/release
+++ b/bin/release
@@ -39,14 +39,14 @@ USAGE()
 {
 cat << EOF
 Usage: $0 -d <dir> [--docver BRANCHNAME] [-h] [--nocheck] [--private] <methods> ...
-   -d DIR               The name of the directory where the releas(es) should be
-                        placed.
+   -d DIR   The name of the directory where the releas(es) should be
+                placed.
    --docver BRANCHNAME  This is added for 1.8 and beyond to get the correct
                         version of documentation files from the hdf5docs
                         repository.  BRANCHNAME for v1.8 should be hdf5_1_8.
-   -h                   print the help page.
-   --nocheck            Ignore errors in MANIFEST file.
-   --private            Make a private release with today's date in version information.
+   -h           print the help page.
+   --nocheck    Ignore errors in MANIFEST file.
+   --private    Make a private release with today's date in version information.
 
 This must be run at the top level of the source directory.
 The other command-line options are the names of the programs to use
@@ -149,8 +149,8 @@ tar2zip()
     find $ztmpdir/$version | \
         while read inf; do \
             if file $inf | grep "$inf\: .*text" > /dev/null 2>&1 ; then \
-            unix2dos -q -k $inf; \
-            fi \
+                unix2dos -q -k $inf; \
+            fi\
         done
     # step 3: make zipball
     # -9 maximum compression
@@ -248,7 +248,7 @@ tar2cmakezip()
         while read inf; do \
             if file $inf | grep "$inf\: .*text" > /dev/null 2>&1 ; then \
                 unix2dos -q -k $inf; \
-            fi \
+            fi\
         done
 
     # step 3: make zipball
@@ -442,7 +442,7 @@ check=yes
 release_date=`date +%F`
 today=`date +%Y%m%d`
 pmode='no'
-tmpdir="../#release_tmp.$$"    # tmp work directory
+tmpdir="../#release_tmp.$$"     # tmp work directory
 DOC_URL=https://git@bitbucket.hdfgroup.org/scm/hdffv/hdf5doc.git
 CPPLUS_RM_NAME=cpplus_RM
 MAINT_MODE_ENABLED=""
@@ -597,17 +597,17 @@ 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; md5sum $HDF5_VERS.tar >> $MD5file)
             ;;
         gzip)
             test "$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; md5sum $HDF5_VERS.tar.gz >> $MD5file)
             ;;
         cmake-tgz)
             test "$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 $DEST; md5sum CMake-$HDF5_VERS.tar.gz >> $MD5file)
             ;;
         hpc-cmake-tgz)
             test "$verbose" && echo "   Creating HPC-CMake tar.gz file..." 1>&2
@@ -617,12 +617,12 @@ for comp in $methods; do
         bzip2)
             test "$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; md5sum $HDF5_VERS.tar.bz2 >> $MD5file)
             ;;
         zip)
             test "$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; md5sum $HDF5_VERS.zip >> $MD5file)
             ;;
         cmake-zip)
             test "$verbose" && echo "   Creating CMake-zip ball..." 1>&2
diff --git a/bin/trace b/bin/trace
index 42b89b5..5fedddb 100755
--- a/bin/trace
+++ b/bin/trace
@@ -165,6 +165,14 @@ $Source = "";
                "ssize_t"                    => "Zs",
               );
 
+
+##############################################################################
+# Maximum length of H5TRACE macro line
+# If the ColumnLimit in .clang-format is changed, this value will need to be updated
+#
+my $max_trace_macro_line_len = 110;
+
+
 ##############################################################################
 # Print an error message.
 #
@@ -242,7 +250,7 @@ sub rewrite_func ($$$$$) {
 
   # Parse arguments
   if ($args eq "void") {
-    $trace = "H5TRACE0(\"$rettype\",\"\");\n";
+    $trace = "H5TRACE0(\"$rettype\", \"\");\n";
   } else {
     # Split arguments.  First convert `/*in,out*/' to get rid of the
     # comma, then split the arguments on commas.
@@ -286,18 +294,34 @@ sub rewrite_func ($$$$$) {
         }
       }
     }
+
+    # Compose the trace macro
     $trace = "H5TRACE" . scalar(@arg_str) . "(\"$rettype\", \"";
     $trace .= join("", @arg_str) . "\"";
-    my $len = 4 + length $trace;
+    my $len = 4 + length $trace;        # Add 4, for indenting the line
     for (@arg_name) {
-      if ($len + length >= 77) {
-        $trace .= ",\n             $_";
-        $len = 13 + length;
+      # Wrap lines that will be longer than the limit, after ');' is added
+      if ($len + length >= ($max_trace_macro_line_len - 2)) {
+        # Wrap line, with indention
+        $trace .= ",\n             ";
+        $len = 13;              # Set to 13, for indention
+
+        # Indent an extra space to account for extra digit in 'H5TRACE' macro
+        if (scalar(@arg_str) >= 10) {
+          $trace .= " ";
+          $len++;
+        }
       } else {
-        $trace .= ", $_";
-        $len += 1 + length;
+        $trace .= ", ";
+        $len += 2;     # Add 2, for ', '
       }
+
+      # Append argument
+      $trace .= "$_";
+      $len += length;     # Add length of appended argument name
     }
+
+    # Append final ');' for macro
     $trace .= ");\n";
   }
   goto error if grep {/!/} @arg_str;