sync bin with develop (#3271)

HDFGroup · Jul 25, 2023 · 2025610 · 2025610
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diff --git a/COPYING b/COPYING
@@ -49,7 +49,7 @@ works thereof, in binary and source code form.
 Limited portions of HDF5 were developed by Lawrence Berkeley National 
 Laboratory (LBNL). LBNL's Copyright Notice and Licensing Terms can be
 found here: COPYING_LBNL_HDF5 file in this directory or at 
-http://support.hdfgroup.org/ftp/HDF5/releases/COPYING_LBNL_HDF5. 
+https://raw.githubusercontent.com/hdfgroup/hdf5/develop/COPYING_LBNL_HDF5. 
 
 -----------------------------------------------------------------------------
 -----------------------------------------------------------------------------

diff --git a/README.md b/README.md
@@ -14,25 +14,26 @@ in science, engineering, and research communities worldwide.
 
 The HDF Group is the developer, maintainer, and steward of HDF5 software. Find more
 information about The HDF Group, the HDF5 Community, and other HDF5 software projects,
-tools, and services at The HDF Group's website.
-
-   https://www.hdfgroup.org/
-
+tools, and services at [The HDF Group's website](https://www.hdfgroup.org/). 
 
 DOCUMENTATION
 -------------
 This release is fully functional for the API described in the documentation.
-    
+
    https://portal.hdfgroup.org/display/HDF5/The+HDF5+API
 
 Full Documentation and Programming Resources for this release can be found at
 
    https://portal.hdfgroup.org/display/HDF5
 
-See the RELEASE.txt file in the release_docs/ directory for information specific
+The latest doxygen documentation generated on changes to develop is available at:
+
+   https://hdfgroup.github.io/hdf5/
+
+See the [RELEASE.txt](/release_docs/RELEASE.txt) file in the [release_docs/](/release_docs/) directory for information specific
 to the features and updates included in this release of the library.
 
-Several more files are located within the release_docs/ directory with specific
+Several more files are located within the [release_docs/](/release_docs/) directory with specific
 details for several common platforms and configurations.
 
     INSTALL - Start Here. General instructions for compiling and installing the library
@@ -52,23 +53,19 @@ Information regarding Help Desk and Support services is available at
 
 FORUM and NEWS
 --------------
-The following public forums are provided for public announcements and discussions
+The [HDF Forum](https://forum.hdfgroup.org) is provided for public announcements and discussions
 of interest to the general HDF5 Community.
 
-   - Homepage of the Forum
-   https://forum.hdfgroup.org
-
-   - News and Announcement
+   - News and Announcements
    https://forum.hdfgroup.org/c/news-and-announcements-from-the-hdf-group
 
-   - HDF5 and HDF4 Topics
+   - HDF5 Topics
    https://forum.hdfgroup.org/c/hdf5
 
 These forums are provided as an open and public service for searching and reading.
 Posting requires completing a simple registration and allows one to join in the
-conversation.  Please read the following instructions pertaining to the Forum's
-use and configuration
-    https://forum.hdfgroup.org/t/quickstart-guide-welcome-to-the-new-hdf-forum
+conversation.  Please read the [instructions](https://forum.hdfgroup.org/t/quickstart-guide-welcome-to-the-new-hdf-forum
+) pertaining to the Forum's use and configuration.
 
 
 

diff --git a/bin/buildhdf5 b/bin/buildhdf5
@@ -12,8 +12,6 @@
 #
 # Build HDF5 library by doing configure, make, and tests.
 # Usage: See USAGE()
-# Programmer: Albert Cheng
-# Creation date: Jul  9, 2003
 
 # Some handy definitions
 USAGE()

diff --git a/bin/chkcopyright b/bin/chkcopyright
@@ -14,10 +14,6 @@
 # Check that all the files have the proper copyright notice.
 # It goes down directories recursively.
 #
-# Programmer: Albert Cheng
-# Created Data: 2003/07/22
-# Modification:
-#	Rewrote most of it. Albert Cheng, 2005/10/10.
 
 # Setup
 #
@@ -363,7 +359,7 @@ MATCH_COPYRIGHT()
 	false
     else
 	if [ $begin -gt 1 ]; then
-	    begin=`expr $begin - 1`
+	    begin=`expr $begin`
 	fi
 	end=`expr $begin + $nlines - 1`
 	sed -n -e "${begin},${end}p" < $f > ${EXTRACTEDFILE}

diff --git a/bin/cmakehdf5 b/bin/cmakehdf5
@@ -1,10 +1,5 @@
-#! /bin/sh
+#!/bin/sh
 # Build and Test HDF5 using cmake.
-# Author: Allen Byrne
-#         Albert Cheng
-# Creation Date: Nov 2012
-# Modified:
-#	Changed to use the quick steps described in INSTALL_CMake.txt. (AKC 2014/1/1)
 
 # Copyright: The HDF Group, 2012-14
 
@@ -365,7 +360,7 @@ STEP "Configure..." \
     $with_zlib \
     $with_szlib \
     $srcdir" $configlog &&\
-    cat $config_summary >> $configlog
+    cat src/$config_summary >> $configlog
 
 #      5. Build the C library, tools and tests with this command:
 STEP "Build the library, tools and tests, ..." "cmake --build . --config Release -- $njobs" $makelog

diff --git a/bin/format_source b/bin/format_source
@@ -5,8 +5,20 @@
 #
 # 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)
+
+COMMAND="clang-format"
+
+if [ $# -eq 1 ]; then
+    COMMAND="$COMMAND-$1"
+fi
+
+echo ""
+echo "bin/format_source <version>"
+echo ""
+echo "Format the HDF5 C source using clang-format. The <version>"
+echo "parameter is optional and can be used to force a specific"
+echo "installed version of clang-format to be used."
+echo ""
 
 find . \( -type d -path ./config -prune -and -not -path ./config \) \
     -or \( \( \! \( \
@@ -21,6 +33,6 @@ find . \( -type d -path ./config -prune -and -not -path ./config \) \
         -or -name H5overflow.h \
         \) \) \
     -and \( -iname *.h -or -iname *.c -or -iname *.cpp -or -iname *.hpp -or -iname *.java \) \) \
-    | xargs clang-format -style=file -i -fallback-style=none
+    | xargs -P0 -n1 ${COMMAND} -style=file -i -fallback-style=none
 
 exit 0
diff --git a/bin/h5vers b/bin/h5vers
@@ -16,8 +16,6 @@ use strict;
 # If you do not have access to either file, you may request a copy from
 # [email protected].
 #
-# Robb Matzke
-# 17 July 1998
 
 ### Purpose
 # Increments the hdf5 version number by changing the value of
@@ -118,8 +116,9 @@ Usage: $prog [OPTS] [FILE]
         as \"version 1.1 release 0 (pre1)\" will be printed.
     FILE
         The name of the file that contains version information.  This is
-        seldom necessary since files H5public.h, src/H5public.h and
-        ../src/H5public.h are automatically checked.
+        seldom necessary since the file H5public.h is checked for current
+        working directory at the top level, one level down, or in the src 
+        directory where H5public.h resides.
 EOF
   exit 1;
 }
@@ -376,7 +375,7 @@ if ($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, $data);
 }
@@ -393,7 +392,7 @@ if ($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/make_err b/bin/make_err
@@ -20,8 +20,6 @@ use warnings;
 # Read in the error description text file and create the appropriate headers
 # needed by the library.
 #
-# Programmer: Quincey Koziol
-# Creation Date: 2003/08/12
 
 ##############################################################################
 # Print the copyright into an open file

diff --git a/bin/make_overflow b/bin/make_overflow
@@ -22,8 +22,6 @@ my @ctypes = ( () );
 
 # Create assignment overflow #ifdefs
 #
-# Programmer: Quincey Koziol
-# Creation Date: 2009/04/09
 
 ##############################################################################
 # Parse a meaningful line (not a comment or blank line) into the appropriate

diff --git a/bin/make_vers b/bin/make_vers
@@ -34,8 +34,6 @@ $indent = 2;
 # Read in the public symbol version description text file and create the
 # appropriate headers needed by the library.
 #
-# Programmer: Quincey Koziol
-# Creation Date: 2007/07/10
 
 ##############################################################################
 # Print the copyright into an open file

diff --git a/bin/output_filter.sh b/bin/output_filter.sh
@@ -11,8 +11,6 @@
 # This contains function definitions of output filtering.
 # This file should only be sourced in by another shell script.
 #
-# Programmer: Albert Cheng
-# Created Date: 2011/5/3
 
 
 # Comment added to address HDFFV-8270:

diff --git a/bin/pkgscrpts/makeInternalREADME.pl b/bin/pkgscrpts/makeInternalREADME.pl
@@ -6,12 +6,10 @@
 #
 # This file is part of HDF4.  The full HDF4 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
-# the files COPYING and Copyright.html.  COPYING can be found at the root
-# of the source code distribution tree; Copyright.html can be found at the
-# root level of an installed copy of the electronic HDF4 document set and
-# is linked from the top-level documents page.  It can also be found at
-# http://hdfgroup.org/HDF4/doc/Copyright.html.  If you do not have
-# access to either file, you may request a copy from [email protected].
+# 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
+# [email protected].
 #
 
 use warnings;

diff --git a/bin/pkgscrpts/makeOuterREADME.pl b/bin/pkgscrpts/makeOuterREADME.pl
@@ -6,12 +6,10 @@
 #
 # This file is part of HDF4.  The full HDF4 copyright notice, including
 # terms governing use, modification, and redistribution, is contained in
-# the files COPYING and Copyright.html.  COPYING can be found at the root
-# of the source code distribution tree; Copyright.html can be found at the
-# root level of an installed copy of the electronic HDF4 document set and
-# is linked from the top-level documents page.  It can also be found at
-# http://hdfgroup.org/HDF4/doc/Copyright.html.  If you do not have
-# access to either file, you may request a copy from [email protected].
+# 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
+# [email protected].
 #
 
 use warnings;

diff --git a/bin/switch_maint_mode b/bin/switch_maint_mode
@@ -12,8 +12,6 @@
 #
 # Switch AM_MAINTAINER_MODE value in configure.ac
 # Usage: See USAGE()
-# Programmer: Dana Robinson
-# Creation date: January 2016
 
 USAGE()
 {

diff --git a/bin/warnhist b/bin/warnhist
@@ -13,9 +13,6 @@ use warnings;
 # If you do not have access to either file, you may request a copy from
 # [email protected].
 #
-# Quincey Koziol
-#  9 Aug 2013
-#
 # Purpose: Given an input file containing the output from a build of the
 #	   library, gather the file names and line numbers, alias
 #          identical types of warnings together into a single bin and