HDF5 1 8 merge of recent changes and tools (#353)

* Update supported platforms

* Merge PR#3 changes from develop

* # WARNING: head commit changed in the meantime

Merge gcc 10 diagnostics option from develop

Merge CMake changes from develop
Merge warnings from develop
Merge #318 OSX changes from develop
Merge tools changes from develop
Merge test macros from develop

* Format updates

* Fix missing semicolon and format fix

* Format update

* Correct actions, remove java option

* Update autotools build files

* Add testfiles

* Fix configure issue with make flags

* Init fapls to default

* Update generated files and fix h5repack id closure

* update format

4 files changed, 129 insertions, 118 deletions

diff --git a/tools/h5jam/Makefile.in b/tools/h5jam/Makefile.in
index 7a60ca3..fdcead9 100644
--- a/tools/h5jam/Makefile.in
+++ b/tools/h5jam/Makefile.in
@@ -420,19 +420,18 @@ AMTAR = @AMTAR@
 
 # H5_CFLAGS holds flags that should be used when building hdf5,
 # but which should not be exported to h5cc for building other programs.
-# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# AM_CFLAGS is an automake construct which should be used by Makefiles
 # instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
 # This applies to FCFLAGS, CXXFLAGS, CPPFLAGS, and LDFLAGS as well.
-AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@ @H5_ECFLAGS@
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
 
 # Include src and tools/lib directories
 AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@ -I$(top_srcdir)/src \
 	-I$(top_srcdir)/tools/lib
-AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@ @H5_ECXXFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
 AM_DEFAULT_VERBOSITY = @AM_DEFAULT_VERBOSITY@
 AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
 AM_LDFLAGS = @AM_LDFLAGS@ @H5_LDFLAGS@
-AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 AUTOCONF = @AUTOCONF@
 AUTOHEADER = @AUTOHEADER@
@@ -463,6 +462,7 @@ DEFS = @DEFS@
 DEPDIR = @DEPDIR@
 DEPRECATED_SYMBOLS = @DEPRECATED_SYMBOLS@
 DEV_WARNINGS = @DEV_WARNINGS@
+DIAGS = @DIAGS@
 DIRECT_VFD = @DIRECT_VFD@
 DLLTOOL = @DLLTOOL@
 DSYMUTIL = @DSYMUTIL@
@@ -490,8 +490,6 @@ GREP = @GREP@
 H5_CFLAGS = @H5_CFLAGS@
 H5_CPPFLAGS = @H5_CPPFLAGS@
 H5_CXXFLAGS = @H5_CXXFLAGS@
-H5_ECFLAGS = @H5_ECFLAGS@
-H5_ECXXFLAGS = @H5_ECXXFLAGS@
 H5_FCFLAGS = @H5_FCFLAGS@
 H5_FORTRAN_SHARED = @H5_FORTRAN_SHARED@
 H5_LDFLAGS = @H5_LDFLAGS@
@@ -670,15 +668,15 @@ LIBH5_HL = $(top_builddir)/hl/src/libhdf5_hl.la
 LIBH5F_HL = $(top_builddir)/hl/fortran/src/libhdf5hl_fortran.la
 LIBH5CPP_HL = $(top_builddir)/hl/c++/src/libhdf5_hl_cpp.la
 
-# Note that in svn revision 19400 the '/' after DESTDIR in H5* variables below  
-# has been removed. According to the official description of DESTDIR by Gnu at 
-# http://www.gnu.org/prep/standards/html_node/DESTDIR.html, DESTDIR is 
-# prepended to the normal and complete install path that it precedes for the 
-# purpose of installing in a temporary directory which is useful for building 
-# rpms and other packages.  The '/' after ${DESTDIR} will be followed by another 
-# '/' at the beginning of the normal install path.  When DESTDIR is empty the  
-# path then begins with '//', which is incorrect and causes problems at least for 
-# Cygwin.   
+# Note that in svn revision 19400 the '/' after DESTDIR in H5* variables below
+# has been removed. According to the official description of DESTDIR by Gnu at
+# http://www.gnu.org/prep/standards/html_node/DESTDIR.html, DESTDIR is
+# prepended to the normal and complete install path that it precedes for the
+# purpose of installing in a temporary directory which is useful for building
+# rpms and other packages.  The '/' after ${DESTDIR} will be followed by another
+# '/' at the beginning of the normal install path.  When DESTDIR is empty the
+# path then begins with '//', which is incorrect and causes problems at least for
+# Cygwin.
 
 # Scripts used to build examples
 # If only shared libraries have been installed, have h5cc build examples with
@@ -724,7 +722,7 @@ LIB = $(lib_LIBRARIES) $(lib_LTLIBRARIES) $(noinst_LIBRARIES)                 \
 PROGS = $(bin_PROGRAMS) $(bin_SCRIPTS) $(noinst_PROGRAMS) $(noinst_SCRIPTS)   \
         $(EXTRA_PROG)
 
-chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST) 
+chk_TESTS = $(check_PROGRAMS) $(check_SCRIPTS) $(EXTRA_TEST)
 TEST_EXTENSIONS = .sh
 SH_LOG_COMPILER = $(SHELL)
 AM_SH_LOG_FLAGS = 
@@ -1254,8 +1252,9 @@ uninstall-am: uninstall-binPROGRAMS
 # commands that should be executed even if a file with the same name already
 # exists.
 .PHONY: build-check-clean build-check-p build-check-s build-lib build-progs \
-        build-tests check-clean check-install check-p check-s check-vfd \
-        install-doc lib progs tests uninstall-doc _exec_check-s _test help
+	build-tests check-clean check-install check-p check-s check-vfd \
+	install-doc lib progs tests uninstall-doc \
+	_exec_check-s _test help
 
 help:
 	@$(top_srcdir)/bin/makehelp
diff --git a/tools/h5jam/h5jam.c b/tools/h5jam/h5jam.c
index a74d79d..1a85f24 100644
--- a/tools/h5jam/h5jam.c
+++ b/tools/h5jam/h5jam.c
@@ -92,13 +92,6 @@ usage(const char *prog)
 static void
 leave(int ret)
 {
-    if (ub_file)
-        HDfree(ub_file);
-    if (input_file)
-        HDfree(input_file);
-    if (output_file)
-        HDfree(output_file);
-
     h5tools_close();
 
     HDexit(ret);
@@ -162,42 +155,40 @@ parse_command_line(int argc, const char *argv[])
 int
 main(int argc, const char *argv[])
 {
-    int         ufid  = -1;
-    int         h5fid = -1;
-    int         ofid  = -1;
-    void *      edata;
-    H5E_auto2_t func;
-    hid_t       ifile = H5I_INVALID_HID;
-    hid_t       plist = H5I_INVALID_HID;
-    herr_t      status;
-    htri_t      testval;
-    hsize_t     usize;
-    hsize_t     h5fsize;
-    hsize_t     startub;
-    hsize_t     where;
-    hsize_t     newubsize;
-    off_t       fsize;
-    h5_stat_t   sbuf;
-    h5_stat_t   sbuf2;
-    int         res;
+    int       ufid  = -1;
+    int       h5fid = -1;
+    int       ofid  = -1;
+    hid_t     ifile = H5I_INVALID_HID;
+    hid_t     plist = H5I_INVALID_HID;
+    herr_t    status;
+    htri_t    testval;
+    hsize_t   usize;
+    hsize_t   h5fsize;
+    hsize_t   startub;
+    hsize_t   where;
+    hsize_t   newubsize;
+    off_t     fsize;
+    h5_stat_t sbuf;
+    h5_stat_t sbuf2;
+    int       res;
 
     h5tools_setprogname(PROGRAMNAME);
     h5tools_setstatus(EXIT_SUCCESS);
 
-    /* Disable error reporting */
-    H5Eget_auto2(H5E_DEFAULT, &func, &edata);
-    H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
-
     /* Initialize h5tools lib */
     h5tools_init();
 
     parse_command_line(argc, argv);
 
+    /* enable error reporting if command line option */
+    h5tools_error_report();
+
     if (ub_file == NULL) {
         /* no user block */
         error_msg("missing argument for -u <user_file>.\n");
         help_ref_msg(stderr);
-        leave(EXIT_FAILURE);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     testval = H5Fis_hdf5(ub_file);
@@ -205,13 +196,15 @@ main(int argc, const char *argv[])
     if (testval > 0) {
         error_msg("-u <user_file> cannot be HDF5 file, but it appears to be an HDF5 file.\n");
         help_ref_msg(stderr);
-        leave(EXIT_FAILURE);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     if (input_file == NULL) {
         error_msg("missing argument for -i <HDF5 file>.\n");
         help_ref_msg(stderr);
-        leave(EXIT_FAILURE);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     testval = H5Fis_hdf5(input_file);
@@ -219,74 +212,76 @@ main(int argc, const char *argv[])
     if (testval <= 0) {
         error_msg("Input HDF5 file \"%s\" is not HDF5 format.\n", input_file);
         help_ref_msg(stderr);
-        leave(EXIT_FAILURE);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     ifile = H5Fopen(input_file, H5F_ACC_RDONLY, H5P_DEFAULT);
 
     if (ifile < 0) {
         error_msg("Can't open input HDF5 file \"%s\"\n", input_file);
-        leave(EXIT_FAILURE);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     plist = H5Fget_create_plist(ifile);
     if (plist < 0) {
         error_msg("Can't get file creation plist for file \"%s\"\n", input_file);
-        H5Fclose(ifile);
-        leave(EXIT_FAILURE);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     status = H5Pget_userblock(plist, &usize);
     if (status < 0) {
         error_msg("Can't get user block for file \"%s\"\n", input_file);
-        H5Pclose(plist);
-        H5Fclose(ifile);
-        leave(EXIT_FAILURE);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     H5Pclose(plist);
+    plist = H5I_INVALID_HID;
     H5Fclose(ifile);
+    ifile = H5I_INVALID_HID;
 
-    ufid = HDopen(ub_file, O_RDONLY, 0);
+    ufid = HDopen(ub_file, O_RDONLY);
     if (ufid < 0) {
         error_msg("unable to open user block file \"%s\"\n", ub_file);
-        leave(EXIT_FAILURE);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     res = HDfstat(ufid, &sbuf);
     if (res < 0) {
         error_msg("Can't stat file \"%s\"\n", ub_file);
-        HDclose(ufid);
-        leave(EXIT_FAILURE);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     fsize = (off_t)sbuf.st_size;
 
-    h5fid = HDopen(input_file, O_RDONLY, 0);
+    h5fid = HDopen(input_file, O_RDONLY);
     if (h5fid < 0) {
         error_msg("unable to open HDF5 file for read \"%s\"\n", input_file);
-        HDclose(ufid);
-        leave(EXIT_FAILURE);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     res = HDfstat(h5fid, &sbuf2);
     if (res < 0) {
         error_msg("Can't stat file \"%s\"\n", input_file);
-        HDclose(h5fid);
-        HDclose(ufid);
-        leave(EXIT_FAILURE);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     h5fsize = (hsize_t)sbuf2.st_size;
 
     if (output_file == NULL) {
-        ofid = HDopen(input_file, O_WRONLY, 0);
+        ofid = HDopen(input_file, O_WRONLY);
 
         if (ofid < 0) {
             error_msg("unable to open output file \"%s\"\n", output_file);
-            HDclose(h5fid);
-            HDclose(ufid);
-            leave(EXIT_FAILURE);
+            h5tools_setstatus(EXIT_FAILURE);
+            goto done;
         }
     }
     else {
@@ -294,9 +289,8 @@ main(int argc, const char *argv[])
 
         if (ofid < 0) {
             error_msg("unable to create output file \"%s\"\n", output_file);
-            HDclose(h5fid);
-            HDclose(ufid);
-            leave(EXIT_FAILURE);
+            h5tools_setstatus(EXIT_FAILURE);
+            goto done;
         }
     }
 
@@ -335,12 +329,11 @@ main(int argc, const char *argv[])
     /* pad the ub */
     if (write_pad(ofid, where, &where) < 0) {
         error_msg("Can't pad file \"%s\"\n", output_file);
-        HDclose(h5fid);
-        HDclose(ufid);
-        HDclose(ofid);
-        leave(EXIT_FAILURE);
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     } /* end if */
 
+done:
     if (ub_file)
         HDfree(ub_file);
     if (input_file)
@@ -348,6 +341,11 @@ main(int argc, const char *argv[])
     if (output_file)
         HDfree(output_file);
 
+    if (plist >= 0)
+        H5Pclose(plist);
+    if (ifile >= 0)
+        H5Fclose(ifile);
+
     if (ufid >= 0)
         HDclose(ufid);
     if (h5fid >= 0)
@@ -355,7 +353,7 @@ main(int argc, const char *argv[])
     if (ofid >= 0)
         HDclose(ofid);
 
-    return h5tools_getstatus();
+    leave(h5tools_getstatus());
 }
 
 /*-------------------------------------------------------------------------
diff --git a/tools/h5jam/h5unjam.c b/tools/h5jam/h5unjam.c
index fff4520..04fd27a 100644
--- a/tools/h5jam/h5unjam.c
+++ b/tools/h5jam/h5unjam.c
@@ -159,6 +159,13 @@ done:
     return EXIT_FAILURE;
 }
 
+static void
+leave(int ret)
+{
+    h5tools_close();
+    HDexit(ret);
+}
+
 /*-------------------------------------------------------------------------
  * Function:    main
  *
@@ -171,30 +178,27 @@ done:
 int
 main(int argc, const char *argv[])
 {
-    void *      edata;
-    H5E_auto2_t func;
-    hid_t       ifile = H5I_INVALID_HID;
-    hid_t       plist = H5I_INVALID_HID;
-    off_t       fsize;
-    hsize_t     usize;
-    htri_t      testval;
-    herr_t      status;
-    int         res;
-    h5_stat_t   sbuf;
+    hid_t     ifile = H5I_INVALID_HID;
+    hid_t     plist = H5I_INVALID_HID;
+    off_t     fsize;
+    hsize_t   usize;
+    htri_t    testval;
+    herr_t    status;
+    int       res;
+    h5_stat_t sbuf;
 
     h5tools_setprogname(PROGRAMNAME);
     h5tools_setstatus(EXIT_SUCCESS);
 
-    /* Disable error reporting  */
-    H5Eget_auto2(H5E_DEFAULT, &func, &edata);
-    H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
-
     /* Initialize h5tools lib  */
     h5tools_init();
 
     if (EXIT_FAILURE == parse_command_line(argc, argv))
         goto done;
 
+    /* enable error reporting if command line option */
+    h5tools_error_report();
+
     if (input_file == NULL) {
         /* no user block  */
         error_msg("missing argument for HDF5 file input.\n");
@@ -293,9 +297,7 @@ done:
         HDfree(ub_file);
     }
 
-    h5tools_close();
-
-    return h5tools_getstatus();
+    leave(h5tools_getstatus());
 }
 
 /*-------------------------------------------------------------------------
diff --git a/tools/h5jam/tellub.c b/tools/h5jam/tellub.c
index ecb67b5..54f545a 100644
--- a/tools/h5jam/tellub.c
+++ b/tools/h5jam/tellub.c
@@ -65,11 +65,12 @@ parse_command_line(int argc, const char *argv[])
         switch ((char)opt) {
             case 'h':
                 usage(h5tools_getprogname());
-                HDexit(EXIT_SUCCESS);
+                h5tools_setstatus(EXIT_SUCCESS);
+                break;
             case '?':
             default:
                 usage(h5tools_getprogname());
-                HDexit(EXIT_FAILURE);
+                h5tools_setstatus(EXIT_FAILURE);
         }
     }
 
@@ -77,10 +78,17 @@ parse_command_line(int argc, const char *argv[])
     if (argc <= opt_ind) {
         error_msg("missing file name\n");
         usage(h5tools_getprogname());
-        HDexit(EXIT_FAILURE);
+        h5tools_setstatus(EXIT_FAILURE);
     }
 } /* end parse_command_line() */
 
+static void
+leave(int ret)
+{
+    h5tools_close();
+    HDexit(ret);
+}
+
 /*-------------------------------------------------------------------------
  * Function:    main
  *
@@ -92,14 +100,12 @@ parse_command_line(int argc, const char *argv[])
 int
 main(int argc, const char *argv[])
 {
-    char *      ifname;
-    void *      edata;
-    H5E_auto2_t func;
-    hid_t       ifile;
-    hsize_t     usize;
-    htri_t      testval;
-    herr_t      status;
-    hid_t       plist = H5I_INVALID_HID;
+    char *  ifname;
+    hid_t   ifile = H5I_INVALID_HID;
+    hsize_t usize;
+    htri_t  testval;
+    herr_t  status;
+    hid_t   plist = H5I_INVALID_HID;
 
     h5tools_setprogname(PROGRAMNAME);
     h5tools_setstatus(EXIT_SUCCESS);
@@ -107,16 +113,16 @@ main(int argc, const char *argv[])
     /* Initialize h5tools lib */
     h5tools_init();
 
-    /* Disable error reporting */
-    H5Eget_auto2(H5E_DEFAULT, &func, &edata);
-    H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
-
     parse_command_line(argc, argv);
 
+    /* enable error reporting if command line option */
+    h5tools_error_report();
+
     if (argc <= (opt_ind)) {
         error_msg("missing file name\n");
         usage(h5tools_getprogname());
-        return EXIT_FAILURE;
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     ifname = HDstrdup(argv[opt_ind]);
@@ -125,32 +131,38 @@ main(int argc, const char *argv[])
 
     if (testval <= 0) {
         error_msg("Input HDF5 file is not HDF \"%s\"\n", ifname);
-        return EXIT_FAILURE;
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     ifile = H5Fopen(ifname, H5F_ACC_RDONLY, H5P_DEFAULT);
 
     if (ifile < 0) {
         error_msg("Can't open input HDF5 file \"%s\"\n", ifname);
-        return EXIT_FAILURE;
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     plist = H5Fget_create_plist(ifile);
     if (plist < 0) {
         error_msg("Can't get file creation plist for file \"%s\"\n", ifname);
-        return EXIT_FAILURE;
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     status = H5Pget_userblock(plist, &usize);
     if (status < 0) {
         error_msg("Can't get user block for file \"%s\"\n", ifname);
-        return EXIT_FAILURE;
+        h5tools_setstatus(EXIT_FAILURE);
+        goto done;
     }
 
     HDprintf("%ld\n", (long)usize);
 
+done:
     H5Pclose(plist);
-    H5Fclose(ifile);
+    if (ifile >= 0)
+        H5Fclose(ifile);
 
-    return EXIT_SUCCESS;
+    leave(h5tools_getstatus());
 } /* end main() */