1.12 Tools merges from develop (#949)

* Tools merges from develop

Brings the tools getopt(3) replacement into the main library (#803)
Perform option arg variables (#834)
Removes unused commented-out code from h5jamgentest.c (#851)
Reorg tools perform to provide h5perf for installation (#884)

* Fix missing files

* Remove empty files

* Remove empty file

* Resync defines

* Fix endif typo

* Add Makfile to list

* Fix typo

* Remove H5_GCC_DIAG_ON line to match removal of H5_GCC_DIAG_OFF line in
sio_engine.c/

Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

1 files changed, 92 insertions, 170 deletions

diff --git a/tools/src/h5dump/h5dump.c b/tools/src/h5dump/h5dump.c
index c9c8185..cab340d 100644
--- a/tools/src/h5dump/h5dump.c
+++ b/tools/src/h5dump/h5dump.c
@@ -80,132 +80,54 @@ struct handler_t {
  */
 /* The following initialization makes use of C language concatenating */
 /* "xxx" "yyy" into "xxxyyy". */
-static const char *        s_opts   = "a:b*c:d:ef:g:hik:l:m:n*o*pq:rs:t:uvw:xyz:A*BCD:E*F:G:HM:N:O*RS:VX:";
-static struct long_options l_opts[] = {{"attribute", require_arg, 'a'},
-                                       {"attribut", require_arg, 'a'},
-                                       {"attribu", require_arg, 'a'},
-                                       {"attrib", require_arg, 'a'},
-                                       {"attri", require_arg, 'a'},
-                                       {"attr", require_arg, 'a'},
-                                       {"att", require_arg, 'a'},
-                                       {"at", require_arg, 'a'},
-                                       {"binary", optional_arg, 'b'},
-                                       {"count", require_arg, 'c'},
-                                       {"coun", require_arg, 'c'},
-                                       {"cou", require_arg, 'c'},
-                                       {"co", require_arg, 'c'},
-                                       {"dataset", require_arg, 'd'},
-                                       {"datase", require_arg, 'd'},
-                                       {"datas", require_arg, 'd'},
-                                       {"escape", no_arg, 'e'},
-                                       {"filedriver", require_arg, 'f'},
-                                       {"filedrive", require_arg, 'f'},
-                                       {"filedriv", require_arg, 'f'},
-                                       {"filedri", require_arg, 'f'},
-                                       {"filedr", require_arg, 'f'},
-                                       {"filed", require_arg, 'f'},
-                                       {"file", require_arg, 'f'},
-                                       {"fil", require_arg, 'f'},
-                                       {"fi", require_arg, 'f'},
-                                       {"group", require_arg, 'g'},
-                                       {"grou", require_arg, 'g'},
-                                       {"gro", require_arg, 'g'},
-                                       {"gr", require_arg, 'g'},
-                                       {"help", no_arg, 'h'},
-                                       {"hel", no_arg, 'h'},
-                                       {"object-ids", no_arg, 'i'},
-                                       {"object-id", no_arg, 'i'},
-                                       {"object-i", no_arg, 'i'},
-                                       {"object", no_arg, 'i'},
-                                       {"objec", no_arg, 'i'},
-                                       {"obje", no_arg, 'i'},
-                                       {"obj", no_arg, 'i'},
-                                       {"ob", no_arg, 'i'},
-                                       {"block", require_arg, 'k'},
-                                       {"bloc", require_arg, 'k'},
-                                       {"blo", require_arg, 'k'},
-                                       {"bl", require_arg, 'k'},
-                                       {"soft-link", require_arg, 'l'},
-                                       {"soft-lin", require_arg, 'l'},
-                                       {"soft-li", require_arg, 'l'},
-                                       {"soft-l", require_arg, 'l'},
-                                       {"soft", require_arg, 'l'},
-                                       {"sof", require_arg, 'l'},
-                                       {"format", require_arg, 'm'},
-                                       {"contents", optional_arg, 'n'},
-                                       {"output", optional_arg, 'o'},
-                                       {"outpu", optional_arg, 'o'},
-                                       {"outp", optional_arg, 'o'},
-                                       {"out", optional_arg, 'o'},
-                                       {"ou", optional_arg, 'o'},
-                                       {"properties", no_arg, 'p'},
-                                       {"sort_by", require_arg, 'q'},
-                                       {"string", no_arg, 'r'},
-                                       {"strin", no_arg, 'r'},
-                                       {"start", require_arg, 's'},
-                                       {"star", require_arg, 's'},
-                                       {"sta", require_arg, 's'},
-                                       {"datatype", require_arg, 't'},
-                                       {"datatyp", require_arg, 't'},
-                                       {"dataty", require_arg, 't'},
-                                       {"datat", require_arg, 't'},
-                                       {"use-dtd", no_arg, 'u'},
-                                       {"use-dt", no_arg, 'u'},
-                                       {"use-d", no_arg, 'u'},
-                                       {"use-", no_arg, 'u'},
-                                       {"use", no_arg, 'u'},
-                                       {"us", no_arg, 'u'},
-                                       {"u", no_arg, 'u'},
-                                       {"vds-view-first-missing", no_arg, 'v'},
-                                       {"width", require_arg, 'w'},
-                                       {"widt", require_arg, 'w'},
-                                       {"wid", require_arg, 'w'},
-                                       {"wi", require_arg, 'w'},
-                                       {"xml", no_arg, 'x'},
-                                       {"xm", no_arg, 'x'},
-                                       {"noindex", no_arg, 'y'},
-                                       {"sort_order", require_arg, 'z'},
-                                       {"onlyattr", optional_arg, 'A'},
-                                       {"superblock", no_arg, 'B'},
-                                       {"boot-block", no_arg, 'B'},
-                                       {"boot-bloc", no_arg, 'B'},
-                                       {"boot-blo", no_arg, 'B'},
-                                       {"boot-bl", no_arg, 'B'},
-                                       {"boot-b", no_arg, 'B'},
-                                       {"boot", no_arg, 'B'},
-                                       {"boo", no_arg, 'B'},
-                                       {"bo", no_arg, 'B'},
-                                       {"no-compact-subset", no_arg, 'C'},
-                                       {"xml-dtd", require_arg, 'D'},
-                                       {"xml-dt", require_arg, 'D'},
-                                       {"xml-d", require_arg, 'D'},
-                                       {"enable-error-stack", optional_arg, 'E'},
-                                       {"form", require_arg, 'F'},
-                                       {"vds-gap-size", require_arg, 'G'},
-                                       {"header", no_arg, 'H'},
-                                       {"heade", no_arg, 'H'},
-                                       {"head", no_arg, 'H'},
-                                       {"hea", no_arg, 'H'},
-                                       {"packed-bits", require_arg, 'M'},
-                                       {"any_path", require_arg, 'N'},
-                                       {"ddl", optional_arg, 'O'},
-                                       {"region", no_arg, 'R'},
-                                       {"stride", require_arg, 'S'},
-                                       {"strid", require_arg, 'S'},
-                                       {"version", no_arg, 'V'},
-                                       {"versio", no_arg, 'V'},
-                                       {"versi", no_arg, 'V'},
-                                       {"vers", no_arg, 'V'},
-                                       {"ver", no_arg, 'V'},
-                                       {"ve", no_arg, 'V'},
-                                       {"xml-ns", require_arg, 'X'},
-                                       {"xml-n", require_arg, 'X'},
-                                       {"s3-cred", require_arg, '$'},
-                                       {"hdfs-attrs", require_arg, '#'},
-                                       {"vol-value", require_arg, '1'},
-                                       {"vol-name", require_arg, '2'},
-                                       {"vol-info", require_arg, '3'},
-                                       {NULL, 0, '\0'}};
+static const char *           s_opts   = "a:b*c:d:ef:g:hik:l:m:n*o*pq:rs:t:uvw:xyz:A*BCD:E*F:G:HM:N:O*RS:VX:";
+static struct h5_long_options l_opts[] = {{"attribute", require_arg, 'a'},
+                                          {"binary", optional_arg, 'b'},
+                                          {"count", require_arg, 'c'},
+                                          {"dataset", require_arg, 'd'},
+                                          {"escape", no_arg, 'e'},
+                                          {"filedriver", require_arg, 'f'},
+                                          {"group", require_arg, 'g'},
+                                          {"help", no_arg, 'h'},
+                                          {"object-ids", no_arg, 'i'},
+                                          {"block", require_arg, 'k'},
+                                          {"soft-link", require_arg, 'l'},
+                                          {"format", require_arg, 'm'},
+                                          {"contents", optional_arg, 'n'},
+                                          {"output", optional_arg, 'o'},
+                                          {"properties", no_arg, 'p'},
+                                          {"sort_by", require_arg, 'q'},
+                                          {"string", no_arg, 'r'},
+                                          {"start", require_arg, 's'},
+                                          {"datatype", require_arg, 't'},
+                                          {"use-dtd", no_arg, 'u'},
+                                          {"vds-view-first-missing", no_arg, 'v'},
+                                          {"width", require_arg, 'w'},
+                                          {"xml", no_arg, 'x'},
+                                          {"noindex", no_arg, 'y'},
+                                          {"sort_order", require_arg, 'z'},
+                                          {"onlyattr", optional_arg, 'A'},
+                                          {"superblock", no_arg, 'B'},
+                                          {"boot-block", no_arg, 'B'},
+                                          {"no-compact-subset", no_arg, 'C'},
+                                          {"xml-dtd", require_arg, 'D'},
+                                          {"enable-error-stack", optional_arg, 'E'},
+                                          {"form", require_arg, 'F'},
+                                          {"vds-gap-size", require_arg, 'G'},
+                                          {"header", no_arg, 'H'},
+                                          {"packed-bits", require_arg, 'M'},
+                                          {"any_path", require_arg, 'N'},
+                                          {"ddl", optional_arg, 'O'},
+                                          {"region", no_arg, 'R'},
+                                          {"stride", require_arg, 'S'},
+                                          {"version", no_arg, 'V'},
+                                          {"xml-ns", require_arg, 'X'},
+                                          {"s3-cred", require_arg, '$'},
+                                          {"hdfs-attrs", require_arg, '#'},
+                                          {"vol-value", require_arg, '1'},
+                                          {"vol-name", require_arg, '2'},
+                                          {"vol-info", require_arg, '3'},
+                                          {NULL, 0, '\0'}};
 
 /*-------------------------------------------------------------------------
  * Function:    leave
@@ -917,7 +839,7 @@ parse_command_line(int argc, const char *argv[])
     }
 
     /* parse command line options */
-    while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+    while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
 parse_start:
         switch ((char)opt) {
             case 'R':
@@ -931,8 +853,8 @@ parse_start:
             case 'n':
                 dump_opts.display_fi = TRUE;
                 last_was_dset        = FALSE;
-                if (opt_arg != NULL)
-                    h5trav_set_verbose(HDatoi(opt_arg));
+                if (H5_optarg != NULL)
+                    h5trav_set_verbose(HDatoi(H5_optarg));
                 break;
             case 'p':
                 dump_opts.display_dcpl = TRUE;
@@ -949,8 +871,8 @@ parse_start:
                 last_was_dset               = FALSE;
                 break;
             case 'A':
-                if (opt_arg != NULL) {
-                    if (0 == HDatoi(opt_arg))
+                if (H5_optarg != NULL) {
+                    if (0 == HDatoi(H5_optarg))
                         dump_opts.include_attrs = FALSE;
                 }
                 else {
@@ -974,7 +896,7 @@ parse_start:
                 goto done;
                 break;
             case 'w': {
-                int sh5tools_nCols = HDatoi(opt_arg);
+                int sh5tools_nCols = HDatoi(H5_optarg);
 
                 if (sh5tools_nCols <= 0)
                     h5tools_nCols = 65535;
@@ -988,7 +910,7 @@ parse_start:
                 for (i = 0; i < argc; i++)
                     if (!hand[i].func) {
                         hand[i].func = handle_paths;
-                        hand[i].obj  = HDstrdup(opt_arg);
+                        hand[i].obj  = HDstrdup(H5_optarg);
                         break;
                     }
 
@@ -1000,7 +922,7 @@ parse_start:
                 for (i = 0; i < argc; i++)
                     if (!hand[i].func) {
                         hand[i].func = handle_attributes;
-                        hand[i].obj  = HDstrdup(opt_arg);
+                        hand[i].obj  = HDstrdup(H5_optarg);
                         break;
                     }
 
@@ -1012,7 +934,7 @@ parse_start:
                 for (i = 0; i < argc; i++)
                     if (!hand[i].func) {
                         hand[i].func        = handle_datasets;
-                        hand[i].obj         = HDstrdup(opt_arg);
+                        hand[i].obj         = HDstrdup(H5_optarg);
                         hand[i].subset_info = parse_subset_params(hand[i].obj);
                         last_dset           = &hand[i];
                         break;
@@ -1021,7 +943,7 @@ parse_start:
                 last_was_dset = TRUE;
                 break;
             case 'f':
-                driver_name_g = opt_arg;
+                driver_name_g = H5_optarg;
                 break;
             case 'g':
                 dump_opts.display_all = 0;
@@ -1029,7 +951,7 @@ parse_start:
                 for (i = 0; i < argc; i++)
                     if (!hand[i].func) {
                         hand[i].func = handle_groups;
-                        hand[i].obj  = HDstrdup(opt_arg);
+                        hand[i].obj  = HDstrdup(H5_optarg);
                         break;
                     }
 
@@ -1041,7 +963,7 @@ parse_start:
                 for (i = 0; i < argc; i++)
                     if (!hand[i].func) {
                         hand[i].func = handle_links;
-                        hand[i].obj  = HDstrdup(opt_arg);
+                        hand[i].obj  = HDstrdup(H5_optarg);
                         break;
                     }
 
@@ -1053,7 +975,7 @@ parse_start:
                 for (i = 0; i < argc; i++)
                     if (!hand[i].func) {
                         hand[i].func = handle_datatypes;
-                        hand[i].obj  = HDstrdup(opt_arg);
+                        hand[i].obj  = HDstrdup(H5_optarg);
                         break;
                     }
 
@@ -1061,7 +983,7 @@ parse_start:
                 break;
 
             case 'O':
-                if (h5tools_set_output_file(opt_arg, 0) < 0) {
+                if (h5tools_set_output_file(H5_optarg, 0) < 0) {
                     usage(h5tools_getprogname());
                     goto error;
                 }
@@ -1069,20 +991,20 @@ parse_start:
 
             case 'o':
                 if (bin_output) {
-                    if (h5tools_set_data_output_file(opt_arg, 1) < 0) {
+                    if (h5tools_set_data_output_file(H5_optarg, 1) < 0) {
                         usage(h5tools_getprogname());
                         goto error;
                     }
                 }
                 else {
                     if (dump_opts.display_attr_data && !dump_opts.display_data) {
-                        if (h5tools_set_attr_output_file(opt_arg, 0) < 0) {
+                        if (h5tools_set_attr_output_file(H5_optarg, 0) < 0) {
                             usage(h5tools_getprogname());
                             goto error;
                         }
                     }
                     if (dump_opts.display_data || dump_opts.display_all) {
-                        if (h5tools_set_data_output_file(opt_arg, 0) < 0) {
+                        if (h5tools_set_data_output_file(H5_optarg, 0) < 0) {
                             usage(h5tools_getprogname());
                             goto error;
                         }
@@ -1091,12 +1013,12 @@ parse_start:
 
                 dump_opts.usingdasho = TRUE;
                 last_was_dset        = FALSE;
-                outfname_g           = opt_arg;
+                outfname_g           = H5_optarg;
                 break;
 
             case 'b':
-                if (opt_arg != NULL) {
-                    if ((bin_form = set_binary_form(opt_arg)) < 0) {
+                if (H5_optarg != NULL) {
+                    if ((bin_form = set_binary_form(H5_optarg)) < 0) {
                         /* failed to set binary form */
                         usage(h5tools_getprogname());
                         goto error;
@@ -1115,7 +1037,7 @@ parse_start:
                 break;
 
             case 'q':
-                if ((sort_by = set_sort_by(opt_arg)) < 0) {
+                if ((sort_by = set_sort_by(H5_optarg)) < 0) {
                     /* failed to set "sort by" form */
                     usage(h5tools_getprogname());
                     goto error;
@@ -1123,7 +1045,7 @@ parse_start:
                 break;
 
             case 'z':
-                if ((sort_order = set_sort_order(opt_arg)) < 0) {
+                if ((sort_order = set_sort_order(H5_optarg)) < 0) {
                     /* failed to set "sort order" form */
                     usage(h5tools_getprogname());
                     goto error;
@@ -1135,7 +1057,7 @@ parse_start:
                     error_msg("option \"-%c\" can only be used after --dataset option\n", opt);
                     goto error;
                 }
-                if (parse_mask_list(opt_arg) != SUCCEED) {
+                if (parse_mask_list(H5_optarg) != SUCCEED) {
                     usage(h5tools_getprogname());
                     goto error;
                 }
@@ -1145,7 +1067,7 @@ parse_start:
                 dump_opts.display_vds_first = TRUE;
                 break;
             case 'G':
-                dump_opts.vds_gap_size = HDatoi(opt_arg);
+                dump_opts.vds_gap_size = HDatoi(H5_optarg);
                 if (dump_opts.vds_gap_size < 0) {
                     usage(h5tools_getprogname());
                     goto error;
@@ -1172,13 +1094,13 @@ parse_start:
             case 'D':
                 /* specify alternative XML DTD or schema */
                 /* To Do: check format of this value?  */
-                xml_dtd_uri_g = opt_arg;
+                xml_dtd_uri_g = H5_optarg;
                 h5tools_nCols = 0;
                 break;
 
             case 'm':
                 /* specify alternative floating point printing format */
-                fp_format     = opt_arg;
+                fp_format     = H5_optarg;
                 h5tools_nCols = 0;
                 break;
 
@@ -1189,10 +1111,10 @@ parse_start:
                     usage(h5tools_getprogname());
                     goto error;
                 }
-                if (HDstrcmp(opt_arg, ":") == 0)
+                if (HDstrcmp(H5_optarg, ":") == 0)
                     xmlnsprefix = "";
                 else
-                    xmlnsprefix = opt_arg;
+                    xmlnsprefix = H5_optarg;
                 h5tools_nCols = 0;
                 break;
             /** end XML parameters **/
@@ -1238,33 +1160,33 @@ parse_start:
                                 HDfree(s->start.data);
                                 s->start.data = NULL;
                             }
-                            parse_hsize_list(opt_arg, &s->start);
+                            parse_hsize_list(H5_optarg, &s->start);
                             break;
                         case 'S':
                             if (s->stride.data) {
                                 HDfree(s->stride.data);
                                 s->stride.data = NULL;
                             }
-                            parse_hsize_list(opt_arg, &s->stride);
+                            parse_hsize_list(H5_optarg, &s->stride);
                             break;
                         case 'c':
                             if (s->count.data) {
                                 HDfree(s->count.data);
                                 s->count.data = NULL;
                             }
-                            parse_hsize_list(opt_arg, &s->count);
+                            parse_hsize_list(H5_optarg, &s->count);
                             break;
                         case 'k':
                             if (s->block.data) {
                                 HDfree(s->block.data);
                                 s->block.data = NULL;
                             }
-                            parse_hsize_list(opt_arg, &s->block);
+                            parse_hsize_list(H5_optarg, &s->block);
                             break;
                         default:
                             goto end_collect;
                     }
-                } while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF);
+                } while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF);
 
 end_collect:
                 last_was_dset = FALSE;
@@ -1277,8 +1199,8 @@ end_collect:
                 /** end subsetting parameters **/
 
             case 'E':
-                if (opt_arg != NULL)
-                    enable_error_stack = HDatoi(opt_arg);
+                if (H5_optarg != NULL)
+                    enable_error_stack = HDatoi(H5_optarg);
                 else
                     enable_error_stack = 1;
                 break;
@@ -1294,7 +1216,7 @@ end_collect:
 
             case '$':
 #ifdef H5_HAVE_ROS3_VFD
-                if (h5tools_parse_ros3_fapl_tuple(opt_arg, ',', &ros3_fa_g) < 0) {
+                if (h5tools_parse_ros3_fapl_tuple(H5_optarg, ',', &ros3_fa_g) < 0) {
                     error_msg("failed to parse S3 VFD credential info\n");
                     usage(h5tools_getprogname());
                     free_handler(hand, argc);
@@ -1311,7 +1233,7 @@ end_collect:
 
             case '#':
 #ifdef H5_HAVE_LIBHDFS
-                if (h5tools_parse_hdfs_fapl_tuple(opt_arg, ',', &hdfs_fa_g) < 0) {
+                if (h5tools_parse_hdfs_fapl_tuple(H5_optarg, ',', &hdfs_fa_g) < 0) {
                     error_msg("failed to parse HDFS VFD configuration info\n");
                     usage(h5tools_getprogname());
                     free_handler(hand, argc);
@@ -1328,18 +1250,18 @@ end_collect:
 
             case '1':
                 vol_info_g.type    = VOL_BY_VALUE;
-                vol_info_g.u.value = (H5VL_class_value_t)HDatoi(opt_arg);
+                vol_info_g.u.value = (H5VL_class_value_t)HDatoi(H5_optarg);
                 use_custom_vol_g   = TRUE;
                 break;
 
             case '2':
                 vol_info_g.type   = VOL_BY_NAME;
-                vol_info_g.u.name = opt_arg;
+                vol_info_g.u.name = H5_optarg;
                 use_custom_vol_g  = TRUE;
                 break;
 
             case '3':
-                vol_info_g.info_string = opt_arg;
+                vol_info_g.info_string = H5_optarg;
                 break;
 
             case '?':
@@ -1351,7 +1273,7 @@ end_collect:
 
 parse_end:
     /* check for file name to be processed */
-    if (argc <= opt_ind) {
+    if (argc <= H5_optind) {
         error_msg("missing file name\n");
         usage(h5tools_getprogname());
         goto error;
@@ -1443,7 +1365,7 @@ main(int argc, const char *argv[])
         }
     }
 
-    if (argc <= opt_ind) {
+    if (argc <= H5_optind) {
         error_msg("missing file name\n");
         usage(h5tools_getprogname());
         h5tools_setstatus(EXIT_FAILURE);
@@ -1496,8 +1418,8 @@ main(int argc, const char *argv[])
         }
     }
 
-    while (opt_ind < argc) {
-        fname = HDstrdup(argv[opt_ind++]);
+    while (H5_optind < argc) {
+        fname = HDstrdup(argv[H5_optind++]);
 
         fid = h5tools_fopen(fname, H5F_ACC_RDONLY, fapl_id, (fapl_id == H5P_DEFAULT) ? FALSE : TRUE, NULL, 0);