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, 111 insertions, 115 deletions

diff --git a/tools/misc/Makefile.in b/tools/misc/Makefile.in
index 31298b7..24e1579 100644
--- a/tools/misc/Makefile.in
+++ b/tools/misc/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 directory
 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
@@ -728,7 +726,7 @@ 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 = 
@@ -1255,8 +1253,9 @@ 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/misc/h5mkgrp.c b/tools/misc/h5mkgrp.c
index f3af4ed..7e92c83 100644
--- a/tools/misc/h5mkgrp.c
+++ b/tools/misc/h5mkgrp.c
@@ -28,15 +28,17 @@ static struct long_options l_opts[] = {{"help", no_arg, 'h'},    {"latest", no_a
                                        {"version", no_arg, 'V'}, {NULL, 0, '\0'}};
 
 /* Command line parameter settings */
-typedef struct {
+typedef struct mkgrp_opt_t {
     char *  fname;   /* File name to operate on */
     hbool_t latest;  /* Whether file should use latest format versions */
     hbool_t verbose; /* Whether output should be verbose */
     hbool_t parents; /* Whether to create intermediate groups */
     size_t  ngroups; /* Number of groups to create */
     char ** groups;  /* Pointer to array of group names */
-} param_t;
-param_t params; /* Command line parameter settings */
+    hid_t   fapl_id; /* fapl to use when opening the file */
+} mkgrp_opt_t;
+
+mkgrp_opt_t params_g; /* Command line parameter settings */
 
 /*-------------------------------------------------------------------------
  * Function:    leave
@@ -54,13 +56,17 @@ leave(int ret)
 {
     size_t curr_group;
 
-    if (params.fname)
-        HDfree(params.fname);
-    if (params.ngroups) {
-        for (curr_group = 0; curr_group < params.ngroups; curr_group++)
-            HDfree(params.groups[curr_group]);
-        HDfree(params.groups);
+    if (params_g.fname)
+        HDfree(params_g.fname);
+    if (params_g.ngroups) {
+        for (curr_group = 0; curr_group < params_g.ngroups; curr_group++)
+            HDfree(params_g.groups[curr_group]);
+        HDfree(params_g.groups);
     }
+    if (H5I_INVALID_HID != params_g.fapl_id && H5P_DEFAULT != params_g.fapl_id)
+        if (H5Pclose(params_g.fapl_id) < 0)
+            error_msg("Could not close file access property list\n");
+
     h5tools_close();
     HDexit(ret);
 } /* end leave() */
@@ -77,64 +83,68 @@ leave(int ret)
  *-------------------------------------------------------------------------
  */
 static void
-usage(void)
+usage(const char *prog)
 {
-    HDfprintf(stdout, "\
-usage: h5mkgrp [OPTIONS] FILE GROUP...\n\
-   OPTIONS\n\
-      -h, --help         Print a usage message and exit\n\
-      -l, --latest       Use latest version of file format to create groups\n\
-      -p, --parents      No error if existing, make parent groups as needed\n\
-      -v, --verbose      Print information about OBJECTS and OPTIONS\n\
-      -V, --version      Print version number and exit\n");
+    FLUSHSTREAM(rawoutstream);
+    PRINTSTREAM(rawoutstream, "usage: %s [OPTIONS] FILE GROUP...\n", prog);
+    PRINTVALSTREAM(rawoutstream, "   OPTIONS\n");
+    PRINTVALSTREAM(rawoutstream, "      -h, --help         Print a usage message and exit\n");
+    PRINTVALSTREAM(rawoutstream,
+                   "      -l, --latest       Use latest version of file format to create groups\n");
+    PRINTVALSTREAM(rawoutstream,
+                   "      -p, --parents      No error if existing, make parent groups as needed\n");
+    PRINTVALSTREAM(rawoutstream, "      -v, --verbose      Print information about OBJECTS and OPTIONS\n");
+    PRINTVALSTREAM(rawoutstream, "      -V, --version      Print version number and exit\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
 } /* end usage() */
 
 /*-------------------------------------------------------------------------
- * Function: parse_command_line
+ * Function:    parse_command_line
  *
- * Purpose: Parses command line and sets up global variable to control output
+ * Purpose:     Parses command line and sets up global variable to control
+ *              output
  *
- * Return:  Success: 0
- *    Failure: -1
+ * Return:      Success: 0
+ *              Failure: -1
  *
  * Programmer: Quincey Koziol, 2/13/2007
  *
  *-------------------------------------------------------------------------
  */
 static int
-parse_command_line(int argc, const char *argv[], param_t *parms)
+parse_command_line(int argc, const char *argv[], mkgrp_opt_t *options)
 {
     int    opt;        /* Option from command line */
     size_t curr_group; /* Current group name to copy */
 
     /* Check for empty command line */
     if (argc == 1) {
-        usage();
+        usage(h5tools_getprogname());
         leave(EXIT_SUCCESS);
-    } /* end if */
+    }
 
     /* Parse command line options */
     while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
         switch ((char)opt) {
             /* Display 'help' */
             case 'h':
-                usage();
+                usage(h5tools_getprogname());
                 leave(EXIT_SUCCESS);
                 break;
 
             /* Create objects with the latest version of the format */
             case 'l':
-                parms->latest = TRUE;
+                options->latest = TRUE;
                 break;
 
             /* Create parent groups */
             case 'p':
-                parms->parents = TRUE;
+                options->parents = TRUE;
                 break;
 
             /* Verbose output */
             case 'v':
-                parms->verbose = TRUE;
+                options->verbose = TRUE;
                 break;
 
             /* Display version */
@@ -145,7 +155,7 @@ parse_command_line(int argc, const char *argv[], param_t *parms)
 
             /* Bad command line argument */
             default:
-                usage();
+                usage(h5tools_getprogname());
                 leave(EXIT_FAILURE);
         } /* end switch */
     }     /* end while */
@@ -153,43 +163,34 @@ parse_command_line(int argc, const char *argv[], param_t *parms)
     /* Check for file name to be processed */
     if (argc <= opt_ind) {
         error_msg("missing file name\n");
-        usage();
+        usage(h5tools_getprogname());
         leave(EXIT_FAILURE);
-    } /* end if */
+    }
 
     /* Retrieve file name */
-    parms->fname = HDstrdup(argv[opt_ind]);
+    options->fname = HDstrdup(argv[opt_ind]);
     opt_ind++;
 
     /* Check for group(s) to be created */
     if (argc <= opt_ind) {
         error_msg("missing group name(s)\n");
-        usage();
+        usage(h5tools_getprogname());
         leave(EXIT_FAILURE);
-    } /* end if */
+    }
 
     /* Allocate space for the group name pointers */
-    parms->ngroups = (size_t)(argc - opt_ind);
-    parms->groups  = (char **)HDmalloc(parms->ngroups * sizeof(char *));
+    options->ngroups = (size_t)(argc - opt_ind);
+    options->groups  = (char **)HDmalloc(options->ngroups * sizeof(char *));
 
     /* Retrieve the group names */
     curr_group = 0;
     while (opt_ind < argc) {
-        parms->groups[curr_group] = HDstrdup(argv[opt_ind]);
+        options->groups[curr_group] = HDstrdup(argv[opt_ind]);
         curr_group++;
         opt_ind++;
-    } /* end while */
-
-#ifdef QAK
-    HDfprintf(stderr, "parms->parents = %t\n", parms->parents);
-    HDfprintf(stderr, "parms->verbose = %t\n", parms->verbose);
-    HDfprintf(stderr, "parms->fname = '%s'\n", parms->fname);
-    HDfprintf(stderr, "parms->ngroups = %Zu\n", parms->ngroups);
-    for (curr_group = 0; curr_group < parms->ngroups; curr_group++)
-        HDfprintf(stderr, "parms->group[%Zu] = '%s'\n", curr_group, parms->groups[curr_group]);
-#endif /* QAK */
-
-    return (0);
+    }
+
+    return 0;
 } /* parse_command_line() */
 
 /*-------------------------------------------------------------------------
@@ -204,117 +205,112 @@ parse_command_line(int argc, const char *argv[], param_t *parms)
 int
 main(int argc, const char *argv[])
 {
-    hid_t  fid;        /* HDF5 file ID */
-    hid_t  fapl_id;    /* File access property list ID */
-    hid_t  lcpl_id;    /* Link creation property list ID */
-    size_t curr_group; /* Current group to create */
+    hid_t  fid     = H5I_INVALID_HID; /* HDF5 file ID */
+    hid_t  lcpl_id = H5I_INVALID_HID; /* Link creation property list ID */
+    size_t curr_group;                /* Current group to create */
 
     h5tools_setprogname(PROGRAMNAME);
     h5tools_setstatus(EXIT_SUCCESS);
 
-    /* Disable the HDF5 library's error reporting */
-    H5Eset_auto2(H5E_DEFAULT, NULL, NULL);
-
     /* Initialize h5tools lib */
     h5tools_init();
 
-    /* Parse command line */
-    HDmemset(&params, 0, sizeof(params));
-    if (parse_command_line(argc, argv, &params) < 0) {
-        error_msg("unable to parse command line arguments\n");
-        leave(EXIT_FAILURE);
-    } /* end if */
+    /* Initialize the parameters */
+    HDmemset(&params_g, 0, sizeof(params_g));
 
     /* Create file access property list */
-    if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+    if ((params_g.fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
         error_msg("Could not create file access property list\n");
         leave(EXIT_FAILURE);
-    } /* end if */
+    }
+
+    /* Parse command line */
+    if (parse_command_line(argc, argv, &params_g) < 0) {
+        error_msg("unable to parse command line arguments\n");
+        leave(EXIT_FAILURE);
+    }
+
+    /* enable error reporting if command line option */
+    h5tools_error_report();
 
     /* Check for creating groups with new format version */
-    if (params.latest) {
+    if (params_g.latest) {
         /* Set the "use the latest version of the format" bounds */
-        if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
+        if (H5Pset_libver_bounds(params_g.fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) {
             error_msg("Could not set property for using latest version of the format\n");
             leave(EXIT_FAILURE);
-        } /* end if */
+        }
 
         /* Display some output if requested */
-        if (params.verbose)
+        if (params_g.verbose)
             HDprintf("%s: Creating groups with latest version of the format\n", h5tools_getprogname());
-    } /* end if */
+    }
 
     /* Attempt to open an existing HDF5 file first */
-    fid = h5tools_fopen(params.fname, H5F_ACC_RDWR, fapl_id, NULL, NULL, 0);
+    fid = h5tools_fopen(params_g.fname, H5F_ACC_RDWR, params_g.fapl_id, FALSE, NULL, 0);
 
     /* If we couldn't open an existing file, try creating file */
     /* (use "EXCL" instead of "TRUNC", so we don't blow away existing non-HDF5 file) */
     if (fid < 0)
-        fid = H5Fcreate(params.fname, H5F_ACC_EXCL, H5P_DEFAULT, fapl_id);
+        fid = H5Fcreate(params_g.fname, H5F_ACC_EXCL, H5P_DEFAULT, params_g.fapl_id);
 
     /* Test for error in opening file */
     if (fid < 0) {
-        error_msg("Could not open output file '%s'\n", params.fname);
+        error_msg("Could not open output file '%s'\n", params_g.fname);
         leave(EXIT_FAILURE);
-    } /* end if */
+    }
 
     /* Create link creation property list */
     if ((lcpl_id = H5Pcreate(H5P_LINK_CREATE)) < 0) {
         error_msg("Could not create link creation property list\n");
         leave(EXIT_FAILURE);
-    } /* end if */
+    }
 
     /* Check for creating intermediate groups */
-    if (params.parents) {
+    if (params_g.parents) {
         /* Set the intermediate group creation property */
         if (H5Pset_create_intermediate_group(lcpl_id, TRUE) < 0) {
             error_msg("Could not set property for creating parent groups\n");
             leave(EXIT_FAILURE);
-        } /* end if */
+        }
 
         /* Display some output if requested */
-        if (params.verbose)
+        if (params_g.verbose)
             HDprintf("%s: Creating parent groups\n", h5tools_getprogname());
-    } /* end if */
+    }
 
     /* Loop over creating requested groups */
-    for (curr_group = 0; curr_group < params.ngroups; curr_group++) {
+    for (curr_group = 0; curr_group < params_g.ngroups; curr_group++) {
         hid_t gid; /* Group ID */
 
         /* Attempt to create a group */
-        if ((gid = H5Gcreate2(fid, params.groups[curr_group], lcpl_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) {
-            error_msg("Could not create group '%s'\n", params.groups[curr_group]);
+        if ((gid = H5Gcreate2(fid, params_g.groups[curr_group], lcpl_id, H5P_DEFAULT, H5P_DEFAULT)) < 0) {
+            error_msg("Could not create group '%s'\n", params_g.groups[curr_group]);
             leave(EXIT_FAILURE);
-        } /* end if */
+        }
 
         /* Close the group */
         if (H5Gclose(gid) < 0) {
-            error_msg("Could not close group '%s'??\n", params.groups[curr_group]);
+            error_msg("Could not close group '%s'??\n", params_g.groups[curr_group]);
             leave(EXIT_FAILURE);
-        } /* end if */
+        }
 
         /* Display some output if requested */
-        if (params.verbose)
-            HDprintf("%s: created group '%s'\n", h5tools_getprogname(), params.groups[curr_group]);
+        if (params_g.verbose)
+            HDprintf("%s: created group '%s'\n", h5tools_getprogname(), params_g.groups[curr_group]);
     } /* end for */
 
     /* Close link creation property list */
     if (H5Pclose(lcpl_id) < 0) {
         error_msg("Could not close link creation property list\n");
         leave(EXIT_FAILURE);
-    } /* end if */
+    }
 
     /* Close file */
     if (H5Fclose(fid) < 0) {
-        error_msg("Could not close output file '%s'??\n", params.fname);
+        error_msg("Could not close output file '%s'??\n", params_g.fname);
         leave(EXIT_FAILURE);
-    } /* end if */
-
-    /* Close file access property list */
-    if (H5Pclose(fapl_id) < 0) {
-        error_msg("Could not close file access property list\n");
-        leave(EXIT_FAILURE);
-    } /* end if */
+    }
 
     leave(EXIT_SUCCESS);
 } /* end main() */
diff --git a/tools/misc/h5repart.c b/tools/misc/h5repart.c
index f13f801..93b6abf 100644
--- a/tools/misc/h5repart.c
+++ b/tools/misc/h5repart.c
@@ -12,7 +12,7 @@
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
 /*
- * Programmer:  Robb Matzke <matzke@llnl.gov>
+ * Programmer:  Robb Matzke
  *              Wednesday, May 13, 1998
  *
  * Purpose:    Repartitions a file family.  This program can be used to
diff --git a/tools/misc/testfiles/h5mkgrp_help.txt b/tools/misc/testfiles/h5mkgrp_help.txt
index ba130f6..2f67c4b 100644
--- a/tools/misc/testfiles/h5mkgrp_help.txt
+++ b/tools/misc/testfiles/h5mkgrp_help.txt
@@ -5,3 +5,4 @@ usage: h5mkgrp [OPTIONS] FILE GROUP...
       -p, --parents      No error if existing, make parent groups as needed
       -v, --verbose      Print information about OBJECTS and OPTIONS
       -V, --version      Print version number and exit
+