Merge pull request #28 from byrnHDF/hdf5_1_12

Hdf5 1 12
HDFGroup · Oct 8, 2020 · 2987442 · 2987442
2 parents 9861543 + ca32c78
commit 2987442
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diff --git a/.clang-format b/.clang-format
@@ -12,7 +12,7 @@ BraceWrapping:
 BreakBeforeBraces: Stroustrup
 BreakAfterJavaFieldAnnotations: true
 BreakStringLiterals: true
-ColumnLimit:     110
+ColumnLimit:     110    # Update $max_trace_macro_line_len in bin/trace also
 IncludeCategories:
   - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
     Priority:        3
@@ -33,6 +33,8 @@ IncludeIsMainRegex: '(public)?$'
 IndentCaseLabels: true
 IndentGotoLabels: false
 IndentWidth:     4
+MacroBlockBegin: "^BEGIN_FUNC"
+MacroBlockEnd: "^END_FUNC"
 ObjCBlockIndentWidth: 4
 ReflowComments:  true
 SortIncludes:    false
@@ -58,5 +60,6 @@ StatementMacros:
   - HMPI_GOTO_ERROR
   - H5_GCC_DIAG_OFF
   - H5_GCC_DIAG_ON
+  - CATCH
 ...
 
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -7,36 +7,36 @@
 # Order is important. The last matching pattern has the most precedence.
 # So if a pull request only touches javascript files, only these owners
 # will be requested to review.
-*.cmake           @byrnHDF
-CMakeLists.txt    @byrnHDF
-CMakeTests.*      @byrnHDF
+*.cmake           @byrnHDF @derobins
+CMakeLists.txt    @byrnHDF @derobins
+CMakeTests.*      @byrnHDF @derobins
 
-/bin/             @lrknox @derobins @byrnHDF
+/bin/             @lrknox @derobins @qkoziol
 
-/c++/             bmribler@hdfgroup.org
+/c++/             @bmribler @byrnHDF
 
-/config/          @lrknox @derobins @byrnHDF
+/config/          @lrknox @derobins @qkoziol @byrnHDF
 
-/doc/             @gnuoyd mainzer@hdfgroup.org
+/doc/             @gnuoyd @jrmainzer
 
-/examples/        @lrknox @derobins bljones@hdfgroup.org
+/examples/        @lrknox @derobins @bljhdf
 
 /fortran/         @brtnfld @epourmal
 
-/hl/              bmribler@hdfgroup.org
+/hl/              @bmribler @byrnHDF
 
 /java/            @jhendersonHDF @byrnHDF
 
 /m4/              @lrknox @derobins
 
-/release_docs/    @lrknox bljones@hdfgroup.org @byrnHDF
+/release_docs/    @lrknox @bljhdf @byrnHDF
 
-/src/             @jhendersonHDF @derobins @fortnern @qkoziol @soumagne @vchoi-hdfgroup mainzer@hdfgroup.org
+/src/             @jhendersonHDF @derobins @fortnern @qkoziol @soumagne @vchoi-hdfgroup @jrmainzer
 
-/test/            @jhendersonHDF @derobins @fortnern @qkoziol @soumagne @vchoi-hdfgroup mainzer@hdfgroup.org
+/test/            @jhendersonHDF @derobins @fortnern @qkoziol @soumagne @vchoi-hdfgroup @jrmainzer
 
-/testpar/         @jhendersonHDF @rawarren mainzer@hdfgroup.org
+/testpar/         @jhendersonHDF @rawarren @jrmainzer @qkoziol
 
-/tools/           @byrnHDF
+/tools/           @byrnHDF @bmribler
 
 /utils/           @lrknox @byrnHDF
diff --git a/.github/workflows/clang-format-check.yml b/.github/workflows/clang-format-check.yml
@@ -8,10 +8,10 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Run clang-format style check for C programs.
-      uses: DoozyX/clang-format-lint-action@v0.8
+      uses: DoozyX/clang-format-lint-action@v0.10
       with:
         source: '.'
-        extensions: 'c,h,cpp'
+        extensions: 'c,h,cpp,hpp'
         clangFormatVersion: 10
         style: file
-        exclude: './config ./hl/src/H5LTanalyze.c'
+        exclude: './config ./hl/src/H5LTanalyze.c ./hl/src/H5LTparse.c ./hl/src/H5LTparse.h ./src/H5Epubgen.h ./src/H5Einit.h ./src/H5Eterm.h ./src/H5Edefin.h ./src/H5version.h ./src/H5overflow.h'
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -95,8 +95,8 @@ jobs:
       if:  matrix.os == 'windows-latest'
       run: |
         # Set these env vars so cmake picks the correct compiler
-        echo "::set-env name=CXX::cl.exe"
-        echo "::set-env name=CC::cl.exe"
+        echo "CXX=cl.exe" >> $GITHUB_ENV
+        echo "CC=cl.exe" >> $GITHUB_ENV
     
     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
     - name: Get Sources

diff --git a/.github/workflows/pr-check.yml b/.github/workflows/pr-check.yml
@@ -89,8 +89,8 @@ jobs:
       if:  matrix.os == 'windows-latest'
       run: |
         # Set these env vars so cmake picks the correct compiler
-        echo "::set-env name=CXX::cl.exe"
-        echo "::set-env name=CC::cl.exe"
+        echo "CXX=cl.exe" >> $GITHUB_ENV
+        echo "CC=cl.exe" >> $GITHUB_ENV
     
     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
     - name: Get Sources

diff --git a/COPYING b/COPYING
@@ -97,10 +97,4 @@ and/or accompanying materials:
 
 -----------------------------------------------------------------------------
 
-HDF5 is available with the SZIP compression library but SZIP is not part 
-of HDF5 and has separate copyright and license terms. See SZIP Compression 
-in HDF Products (www.hdfgroup.org/doc_resource/SZIP/) for further details.
-
------------------------------------------------------------------------------
-
 
diff --git a/MANIFEST b/MANIFEST
@@ -3452,7 +3452,6 @@
 ./config/cmake/HDFCompilerFlags.cmake
 ./config/cmake/HDFCXXCompilerFlags.cmake
 ./config/cmake/HDFFortranCompilerFlags.cmake
-./config/cmake/HDF5_Process_Flex_Files.cmake
 ./config/cmake/HDF5Macros.cmake
 ./config/cmake/HDF5UseFortran.cmake
 ./config/cmake/jrunTest.cmake

diff --git a/bin/errors b/bin/errors
@@ -17,7 +17,7 @@ use Text::Tabs;
 # 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
 # 30 Aug 1997
 #
 # Purpose: This script will read standard input which should be a

diff --git 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
+exit 0
diff --git 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
+exit 0
diff --git 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
@@ -200,25 +200,29 @@ 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.
 #
 # Note that the GCC pragmas did not exist until gcc 4.2. Earlier versions
 # 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
@@ -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/trace b/bin/trace
@@ -210,6 +210,14 @@ $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.
 #
@@ -287,7 +295,7 @@ 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.
@@ -331,18 +339,34 @@ 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;

diff --git a/bin/warnhist b/bin/warnhist
@@ -15,7 +15,7 @@ use warnings;
 # http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have
 # access to either file, you may request a copy from help@hdfgroup.org.
 #
-# Quincey Koziol, koziol@hdfgroup.org
+# Quincey Koziol
 #  9 Aug 2013
 #
 # Purpose: Given an input file containing the output from a build of the