Merge from develop

github updates
bin scripts
parser updates

6 files changed, 169 insertions, 75 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/h5vers b/bin/h5vers
index c8abef8..55e6bf9 100755
--- a/bin/h5vers
+++ b/bin/h5vers
@@ -17,7 +17,7 @@ use strict;
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 #
-# Robb Matzke <matzke@llnl.gov>
+# Robb Matzke
 # 17 July 1998
 
 ### Purpose
diff --git a/bin/pkgscrpts/h5rmflags b/bin/pkgscrpts/h5rmflags
index 80a249e..099956c 100755
--- a/bin/pkgscrpts/h5rmflags
+++ b/bin/pkgscrpts/h5rmflags
@@ -12,11 +12,9 @@
 # help@hdfgroup.org.
 #
 
-## This script wasextracted from h5redeploy to find hdf5 compile scripts and 
-## remove build paths from hdf5 compile scripts.  Script is intended to be 
-## called from the make18xxTarFiles.pl script, so it could be stripped of options.
-## Actions are predetermined and written in this script instead of in a command
-## file.
+## Remove paths to libraries used to build HDF5 when packaging HDF5
+## binaries.
+## For help page, use "h5rmflags -help"
 
 # Constants definitions
 EXIT_SUCCESS=0
diff --git a/bin/trace b/bin/trace
index 8b3f68e..7ca84e6 100755
--- a/bin/trace
+++ b/bin/trace
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 ##
 # Copyright by The HDF Group.
 # Copyright by the Board of Trustees of the University of Illinois.
@@ -12,6 +12,7 @@
 # help@hdfgroup.org.
 ##
 require 5.003;
+use warnings;
 $Source = "";
 
 ##############################################################################
@@ -30,28 +31,29 @@ $Source = "";
                "hbool_t"                    => "b",
                "double"                     => "d",
                "H5D_alloc_time_t"           => "Da",
-	       "H5FD_mpio_collective_opt_t" => "Dc",
+               "H5FD_mpio_collective_opt_t" => "Dc",
                "H5D_fill_time_t"            => "Df",
                "H5D_fill_value_t"           => "DF",
-	       "H5FD_mpio_chunk_opt_t"      => "Dh",
+               "H5FD_mpio_chunk_opt_t"      => "Dh",
                "H5D_mpio_actual_io_mode_t"  => "Di",
                "H5D_layout_t"               => "Dl",
                "H5D_mpio_no_collective_cause_t" => "Dn",
                "H5D_mpio_actual_chunk_opt_mode_t" => "Do",
                "H5D_space_status_t"         => "Ds",
                "H5FD_mpio_xfer_t"           => "Dt",
+               "H5FD_splitter_vfd_config_t" => "Dr",
                "herr_t"                     => "e",
                "H5E_direction_t"            => "Ed",
                "H5E_error_t"                => "Ee",
-	       "H5E_type_t"                 => "Et",
-	       "H5F_close_degree_t"         => "Fd",
+               "H5E_type_t"                 => "Et",
+               "H5F_close_degree_t"         => "Fd",
                "H5F_scope_t"                => "Fs",
-	       "H5F_libver_t"               => "Fv",
+               "H5F_libver_t"               => "Fv",
                "H5G_obj_t"                  => "Go",
                "H5G_stat_t"                 => "Gs",
-	       "hsize_t"                    => "h",
+               "hsize_t"                    => "h",
                "hssize_t"                   => "Hs",
-	       "H5E_major_t"                => "i",
+               "H5E_major_t"                => "i",
                "H5E_minor_t"                => "i",
                "H5_iter_order_t"            => "Io",
                "H5_index_t"                 => "Ii",
@@ -61,16 +63,17 @@ $Source = "";
                "unsigned"                   => "Iu",
                "unsigned int"               => "Iu",
                "uint32_t"                   => "Iu",
+               "uint64_t"                   => "UL",
                "H5I_type_t"                 => "It",
-	       "H5G_link_t"                 => "Ll", #Same as H5L_type_t now
-	       "H5L_type_t"                 => "Ll",
+               "H5G_link_t"                 => "Ll", #Same as H5L_type_t now
+               "H5L_type_t"                 => "Ll",
                "MPI_Comm"                   => "Mc",
                "MPI_Info"                   => "Mi",
                "H5FD_mem_t"                 => "Mt",
                "off_t"                      => "o",
                "H5O_type_t"                 => "Ot",
                "H5P_class_t"                => "p",
-	       "hobj_ref_t"		    => "r",
+               "hobj_ref_t"                 => "r",
                "H5R_type_t"                 => "Rt",
                "char"                       => "s",
                "unsigned char"              => "s",
@@ -92,9 +95,9 @@ $Source = "";
                "void"                       => "x",
                "FILE"                       => "x",
                "H5A_operator_t"             => "x",
-	       "H5A_operator1_t"            => "x",
-	       "H5A_operator2_t"            => "x",
-	       "H5A_info_t"                 => "x",
+               "H5A_operator1_t"            => "x",
+               "H5A_operator2_t"            => "x",
+               "H5A_info_t"                 => "x",
                "H5AC_cache_config_t"        => "x",
                "H5D_gather_func_t"          => "x",
                "H5D_operator_t"             => "x",
@@ -105,21 +108,24 @@ $Source = "";
                "H5E_walk_t"                 => "x",
                "H5E_walk1_t"                => "x",
                "H5E_walk2_t"                => "x",
-	       "H5F_info_t"                 => "x",
+               "H5F_info_t"                 => "x",
                "H5FD_t"                     => "x",
                "H5FD_class_t"               => "x",
                "H5FD_stream_fapl_t"         => "x",
+               "H5FD_ros3_fapl_t"           => "x",
+               "H5FD_hdfs_fapl_t"           => "x",
                "H5FD_file_image_callbacks_t" => "x",
+               "H5FD_mirror_fapl_t"         => "x",
                "H5G_iterate_t"              => "x",
-	       "H5G_info_t"                 => "x",
-	       "H5I_free_t"                 => "x",
-                "H5I_search_func_t"         => "x",
-                "H5L_class_t"                => "x",
+               "H5G_info_t"                 => "x",
+               "H5I_free_t"                 => "x",
+               "H5I_search_func_t"          => "x",
+               "H5L_class_t"                => "x",
                "H5L_elink_traverse_t"       => "x",
                "H5L_iterate_t"              => "x",
                "H5MM_allocate_t"            => "x",
                "H5MM_free_t"                => "x",
-	       "H5O_info_t"                 => "x",
+               "H5O_info_t"                 => "x",
                "H5O_iterate_t"              => "x",
                "H5O_mcdt_search_cb_t"       => "x",
                "H5P_cls_create_func_t"      => "x",
@@ -147,9 +153,19 @@ $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.
 #
+my $found_errors = 0;
+
 sub errmesg ($$@) {
   my ($file, $func, @mesg) = @_;
   my ($mesg) = join "", @mesg;
@@ -159,6 +175,8 @@ sub errmesg ($$@) {
     $lineno = tr/\n/\n/;
   }
 
+  $found_errors = 1;
+
   print "$file: in function \`$func\':\n";
   print "$file:$lineno: $mesg\n";
 }
@@ -175,6 +193,11 @@ sub argstring ($$$) {
   # certain type qualifiers, and indirection.
   $atype =~ s/^\bconst\b//;
   $atype =~ s/\bH5_ATTR_UNUSED\b//g;
+  $atype =~ s/\bH5_ATTR_DEPRECATED_USED\b//g;
+  $atype =~ s/\bH5_ATTR_NDEBUG_UNUSED\b//g;
+  $atype =~ s/\bH5_ATTR_DEBUG_API_USED\b//g;
+  $atype =~ s/\bH5_ATTR_PARALLEL_UNUSED\b//g;
+  $atype =~ s/\bH5_ATTR_PARALLEL_USED\b//g;
   $atype =~ s/\s+/ /g;
   $ptr = length $1 if  $atype =~ s/(\*+)//;
   $atype =~ s/^\s+//;
@@ -215,7 +238,7 @@ sub rewrite_func ($$$$$) {
 
   # 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.
@@ -229,48 +252,64 @@ sub rewrite_func ($$$$$) {
         next;
       }
       unless ($arg=~/^(([a-z_A-Z]\w*\s+)+\**)
-	      ([a-z_A-Z]\w*)(\[.*?\])?
-	      (\s*\/\*\s*(in|out|in_out)\s*\*\/)?\s*$/x) {
-	errmesg $file, $name, "unable to parse \`$arg\'";
-	goto error;
+              ([a-z_A-Z]\w*)(\[.*?\])?
+              (\s*\/\*\s*(in|out|in_out)\s*\*\/)?\s*$/x) {
+        errmesg $file, $name, "unable to parse \`$arg\'";
+        goto error;
       } else {
-	my ($atype, $aname, $array, $adir) = ($1, $3, $4, $6);
-	$names{$aname} = $argno++;
-	$adir ||= "in";
-	$atype =~ s/\s+$//;
-	push @arg_name, $aname;
+        my ($atype, $aname, $array, $adir) = ($1, $3, $4, $6);
+        $names{$aname} = $argno++;
+        $adir ||= "in";
+        $atype =~ s/\s+$//;
+        push @arg_name, $aname;
 
-	if ($adir eq "out") {
-	  push @arg_str, "x";
-	} else {
-	  if (defined $array) {
-	    $atype .= "*";
-	    if ($array =~ /^\[\/\*([a-z_A-Z]\w*)\*\/\]$/) {
-	      my $asize = $1;
-	      if (exists $names{$asize}) {
-		$atype .= '[a' . $names{$asize} . ']';
-	      } else {
-		warn "bad array size: $asize";
-		$atype .= "*";
-	      }
-	    }
-	  }
-	  push @arg_str, argstring $file, $name, $atype;
-	}
+        if ($adir eq "out") {
+          push @arg_str, "x";
+        } else {
+          if (defined $array) {
+            $atype .= "*";
+            if ($array =~ /^\[\/\*([a-z_A-Z]\w*)\*\/\]$/) {
+              my $asize = $1;
+              if (exists $names{$asize}) {
+                $atype .= '[a' . $names{$asize} . ']';
+              } else {
+                warn "bad array size: $asize";
+                $atype .= "*";
+              }
+            }
+          }
+          push @arg_str, argstring $file, $name, $atype;
+        }
       }
     }
+
+    # 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;
@@ -280,7 +319,7 @@ sub rewrite_func ($$$$$) {
     # Ignored due to NO TRACE comment.
   } elsif ($body =~ s/((\n[ \t]*)H5TRACE\d+\s*\(.*?\);)\n/"$2$trace"/es) {
     # Replaced an H5TRACE macro.
-  } elsif ($body=~s/((\n[ \t]*)FUNC_ENTER\w*\s*(\(.*?\))?;??)\n/"$1$2$trace"/es) {
+  } elsif ($body=~s/((\n[ \t]*)FUNC_ENTER\w*[ \t]*(\(.*?\))?;??)\n/"$1$2$trace"/es) {
     # Added an H5TRACE macro after a FUNC_ENTER macro.
   } else {
     errmesg $file, $name, "unable to insert tracing information";
@@ -328,5 +367,13 @@ for $file (@ARGV) {
   }
 }
 
-printf "Finished processing HDF5 API calls\n"
+if ($found_errors eq 1) {
+    printf "\n";
+    printf "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n";
+    printf "*** ERRORS FOUND *** ERRORS FOUND *** ERRORS FOUND ****\n";
+    printf "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n";
+    exit 1;
+} else {
+    printf "Finished processing HDF5 API calls\n";
+}