1 12 merge of changes from dev (#271)

* OESS-98 fix tools test for plugins

* sync fork

* Merge of changes from dev

* Move problem option to bottom of the list until fixed

* HDFFV-11106 - fix parsing optional args

* HDFFV-11106 add note

* grammer fix

10 files changed, 117 insertions, 113 deletions

diff --git a/tools/lib/h5tools_utils.c b/tools/lib/h5tools_utils.c
index aa2418d..9c5999b 100644
--- a/tools/lib/h5tools_utils.c
+++ b/tools/lib/h5tools_utils.c
@@ -194,44 +194,50 @@ get_option(int argc, const char **argv, const char *opts, const struct long_opti
 
     if (sp == 1 && argv[opt_ind][0] == '-' && argv[opt_ind][1] == '-') {
         /* long command line option */
-        const char *arg = &argv[opt_ind][2];
         int         i;
+        const char  ch = '=';
+        char *arg = &argv[opt_ind][2];
+        size_t arg_len = 0;
+
+        opt_arg = strchr(&argv[opt_ind][2], ch);
+        arg_len = HDstrlen(&argv[opt_ind][2]);
+        if (opt_arg) {
+            arg_len -= HDstrlen(opt_arg);
+            opt_arg++; /* skip the equal sign */
+        }
+        arg[arg_len] = 0;
 
         for (i = 0; l_opts && l_opts[i].name; i++) {
             size_t len = HDstrlen(l_opts[i].name);
 
-            if (HDstrncmp(arg, l_opts[i].name, len) == 0) {
+            if (HDstrcmp(arg, l_opts[i].name) == 0) {
                 /* we've found a matching long command line flag */
                 opt_opt = l_opts[i].shortval;
 
                 if (l_opts[i].has_arg != no_arg) {
-                    if (arg[len] == '=') {
-                        opt_arg = &arg[len + 1];
-                    }
-                    else if (l_opts[i].has_arg != optional_arg) {
-                        if (opt_ind < (argc - 1))
-                            if (argv[opt_ind + 1][0] != '-')
-                                opt_arg = argv[++opt_ind];
-                    }
-                    else if (l_opts[i].has_arg == require_arg) {
-                        if (opt_err)
-                            HDfprintf(rawerrorstream, "%s: option required for \"--%s\" flag\n", argv[0],
-                                      arg);
-
-                        opt_opt = '?';
+                    if (opt_arg == NULL) {
+                        if (l_opts[i].has_arg != optional_arg) {
+                            if (opt_ind < (argc - 1))
+                                if (argv[opt_ind + 1][0] != '-')
+                                    opt_arg = argv[++opt_ind];
+                        }
+                        else if (l_opts[i].has_arg == require_arg) {
+                            if (opt_err)
+                                HDfprintf(rawerrorstream, "%s: option required for \"--%s\" flag\n", argv[0],
+                                        arg);
+
+                            opt_opt = '?';
+                        }
                     }
-                    else
-                        opt_arg = NULL;
                 }
                 else {
-                    if (arg[len] == '=') {
+                    if (opt_arg) {
                         if (opt_err)
                             HDfprintf(rawerrorstream, "%s: no option required for \"%s\" flag\n", argv[0],
                                       arg);
 
                         opt_opt = '?';
                     }
-                    opt_arg = NULL;
                 }
                 break;
             }
diff --git a/tools/src/h5diff/h5diff_common.c b/tools/src/h5diff/h5diff_common.c
index 95245bd..5646e2a 100644
--- a/tools/src/h5diff/h5diff_common.c
+++ b/tools/src/h5diff/h5diff_common.c
@@ -25,7 +25,7 @@ static int check_d_input(const char *);
  * Command-line options: The user can specify short or long-named
  * parameters.
  */
-static const char *        s_opts   = "hVrv:qn:d:p:NcelxE:A:S";
+static const char *        s_opts   = "hVrv*qn:d:p:NcelxE:A:S";
 static struct long_options l_opts[] = {{"help", no_arg, 'h'},
                                        {"version", no_arg, 'V'},
                                        {"report", no_arg, 'r'},
@@ -253,33 +253,27 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
 
             case 'v':
                 opts->mode_verbose = 1;
-                /* This for loop is for handling style like
-                 * -v, -v1, --verbose, --verbose=1.
-                 */
                 for (i = 1; i < argc; i++) {
                     /*
-                     * short opt
+                     * special check for short opt
                      */
-                    if (!strcmp(argv[i], "-v")) { /* no arg */
-                        opt_ind--;
+                    if (!strcmp(argv[i], "-v")) {
+                        if (opt_arg != NULL)
+                            opt_ind--;
                         opts->mode_verbose_level = 0;
                         break;
                     }
                     else if (!strncmp(argv[i], "-v", (size_t)2)) {
+                        if (opt_arg != NULL)
+                            opt_ind--;
                         opts->mode_verbose_level = atoi(&argv[i][2]);
                         break;
                     }
-
-                    /*
-                     * long opt
-                     */
-                    if (!strcmp(argv[i], "--verbose")) { /* no arg */
-                        opts->mode_verbose_level = 0;
-                        break;
-                    }
-                    else if (!strncmp(argv[i], "--verbose", (size_t)9) && argv[i][9] == '=') {
-                        opts->mode_verbose_level = atoi(&argv[i][10]);
-                        break;
+                    else {
+                        if (opt_arg != NULL)
+                            opts->mode_verbose_level = HDatoi(opt_arg);
+                        else
+                            opts->mode_verbose_level = 0;
                     }
                 }
                 break;
diff --git a/tools/src/h5dump/h5dump.c b/tools/src/h5dump/h5dump.c
index 34b3c10..1429842 100644
--- a/tools/src/h5dump/h5dump.c
+++ b/tools/src/h5dump/h5dump.c
@@ -80,39 +80,8 @@ struct handler_t {
  */
 /* The following initialization makes use of C language concatenating */
 /* "xxx" "yyy" into "xxxyyy". */
-static const char *        s_opts   = "hn*peyBHirVa:c:d:f:g:k:l:t:w:xD:uX:o*b*F:s:S:A*q:z:m:RE*CM:O*N:vG:";
-static struct long_options l_opts[] = {{"help", no_arg, 'h'},
-                                       {"hel", no_arg, 'h'},
-                                       {"contents", optional_arg, 'n'},
-                                       {"properties", no_arg, 'p'},
-                                       {"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'},
-                                       {"header", no_arg, 'H'},
-                                       {"heade", no_arg, 'H'},
-                                       {"head", no_arg, 'H'},
-                                       {"hea", 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'},
-                                       {"version", no_arg, 'V'},
-                                       {"versio", no_arg, 'V'},
-                                       {"versi", no_arg, 'V'},
-                                       {"vers", no_arg, 'V'},
-                                       {"ver", no_arg, 'V'},
-                                       {"ve", no_arg, 'V'},
-                                       {"attribute", require_arg, 'a'},
+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'},
@@ -120,10 +89,7 @@ static struct long_options l_opts[] = {{"help", no_arg, 'h'},
                                        {"attr", require_arg, 'a'},
                                        {"att", require_arg, 'a'},
                                        {"at", require_arg, 'a'},
-                                       {"block", require_arg, 'k'},
-                                       {"bloc", require_arg, 'k'},
-                                       {"blo", require_arg, 'k'},
-                                       {"bl", require_arg, 'k'},
+                                       {"binary", optional_arg, 'b'},
                                        {"count", require_arg, 'c'},
                                        {"coun", require_arg, 'c'},
                                        {"cou", require_arg, 'c'},
@@ -131,10 +97,7 @@ static struct long_options l_opts[] = {{"help", no_arg, 'h'},
                                        {"dataset", require_arg, 'd'},
                                        {"datase", require_arg, 'd'},
                                        {"datas", require_arg, 'd'},
-                                       {"datatype", require_arg, 't'},
-                                       {"datatyp", require_arg, 't'},
-                                       {"dataty", require_arg, 't'},
-                                       {"datat", require_arg, 't'},
+                                       {"escape", no_arg, 'e'},
                                        {"filedriver", require_arg, 'f'},
                                        {"filedrive", require_arg, 'f'},
                                        {"filedriv", require_arg, 'f'},
@@ -148,24 +111,44 @@ static struct long_options l_opts[] = {{"help", no_arg, 'h'},
                                        {"grou", require_arg, 'g'},
                                        {"gro", require_arg, 'g'},
                                        {"gr", require_arg, 'g'},
-                                       {"output", optional_arg, 'o'},
-                                       {"outpu", optional_arg, 'o'},
-                                       {"outp", optional_arg, 'o'},
-                                       {"out", optional_arg, 'o'},
-                                       {"ou", optional_arg, 'o'},
+                                       {"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'},
-                                       {"stride", require_arg, 'S'},
-                                       {"strid", require_arg, 'S'},
-                                       {"string", no_arg, 'r'},
-                                       {"strin", no_arg, 'r'},
+                                       {"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'},
@@ -173,33 +156,50 @@ static struct long_options l_opts[] = {{"help", no_arg, 'h'},
                                        {"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-dtd", require_arg, 'D'},
-                                       {"xml-dt", require_arg, 'D'},
-                                       {"xml-d", require_arg, 'D'},
-                                       {"xml-ns", require_arg, 'X'},
-                                       {"xml-n", require_arg, 'X'},
                                        {"xml", no_arg, 'x'},
                                        {"xm", no_arg, 'x'},
-                                       {"onlyattr", optional_arg, 'A'},
-                                       {"escape", no_arg, 'e'},
                                        {"noindex", no_arg, 'y'},
-                                       {"binary", optional_arg, 'b'},
-                                       {"form", require_arg, 'F'},
-                                       {"sort_by", require_arg, 'q'},
                                        {"sort_order", require_arg, 'z'},
-                                       {"format", require_arg, 'm'},
-                                       {"region", no_arg, 'R'},
+                                       {"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'},
-                                       {"no-compact-subset", no_arg, 'C'},
-                                       {"ddl", optional_arg, 'O'},
                                        {"any_path", require_arg, 'N'},
-                                       {"vds-view-first-missing", no_arg, 'v'},
-                                       {"vds-gap-size", require_arg, 'G'},
+                                       {"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'},
diff --git a/tools/src/h5dump/h5dump.h b/tools/src/h5dump/h5dump.h
index b4198ad..9392ca3 100644
--- a/tools/src/h5dump/h5dump.h
+++ b/tools/src/h5dump/h5dump.h
@@ -83,7 +83,7 @@ typedef struct {
 dump_opt_t dump_opts = {TRUE, FALSE, TRUE,  TRUE,  FALSE, FALSE, FALSE, FALSE, FALSE,
                         TRUE, FALSE, FALSE, FALSE, FALSE, TRUE,  FALSE, 0};
 
-#define PACKED_BITS_MAX      8                       /* Maximum number of packed-bits to display */
+#define PACKED_BITS_MAX      8 /* Maximum number of packed-bits to display */
 #define PACKED_BITS_SIZE_MAX (8 * sizeof(long long)) /* Maximum bits size of integer types of packed-bits */
 /* mask list for packed bits */
 unsigned long long packed_mask[PACKED_BITS_MAX]; /* packed bits are restricted to 8*sizeof(llong) bytes */
diff --git a/tools/src/h5dump/h5dump_extern.h b/tools/src/h5dump/h5dump_extern.h
index 6ccd159..56734cf 100644
--- a/tools/src/h5dump/h5dump_extern.h
+++ b/tools/src/h5dump/h5dump_extern.h
@@ -80,7 +80,7 @@ typedef struct {
 } dump_opt_t;
 extern dump_opt_t dump_opts;
 
-#define PACKED_BITS_MAX      8                     /* Maximum number of packed-bits to display */
+#define PACKED_BITS_MAX      8 /* Maximum number of packed-bits to display */
 #define PACKED_BITS_SIZE_MAX 8 * sizeof(long long) /* Maximum bits size of integer types of packed-bits */
 /* mask list for packed bits */
 extern unsigned long long
diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c
index c38dd66..a67d6ac 100644
--- a/tools/src/h5repack/h5repack_main.c
+++ b/tools/src/h5repack/h5repack_main.c
@@ -262,6 +262,7 @@ usage(const char *prog)
     PRINTVALSTREAM(rawoutstream,
                    "            Required values: filter_number, filter_flag, cd_value_count, value1\n");
     PRINTVALSTREAM(rawoutstream, "            Optional values: value2 to valueN\n");
+    PRINTVALSTREAM(rawoutstream, "            filter_flag: 1 is OPTIONAL or 0 is MANDATORY\n");
     PRINTVALSTREAM(rawoutstream, "        NONE (no parameter)\n");
     PRINTVALSTREAM(rawoutstream, "\n");
     PRINTVALSTREAM(rawoutstream, "    LAYT - is a string with the format:\n");
diff --git a/tools/src/misc/h5debug.c b/tools/src/misc/h5debug.c
index 85abb8a..9236828 100644
--- a/tools/src/misc/h5debug.c
+++ b/tools/src/misc/h5debug.c
@@ -67,7 +67,6 @@
  * Return:  Non-NULL on success/NULL on failure
  *
  * Programmer:  Quincey Koziol
- *    koziol@hdfgroup.org
  *    Sep 11 2008
  *
  *-------------------------------------------------------------------------
@@ -149,7 +148,6 @@ get_H5B2_class(const uint8_t *sig)
  * Return:  Non-NULL on success/NULL on failure
  *
  * Programmer:  Quincey Koziol
- *    koziol@hdfgroup.org
  *    Sep 11 2008
  *
  *-------------------------------------------------------------------------
@@ -191,7 +189,6 @@ get_H5EA_class(const uint8_t *sig)
  * Return:  Non-NULL on success/NULL on failure
  *
  * Programmer:  Quincey Koziol
- *    koziol@hdfgroup.org
  *    Sep 11 2008
  *
  *-------------------------------------------------------------------------
diff --git a/tools/test/h5jam/getub.c b/tools/test/h5jam/getub.c
index 9e9cd4d..80e0c66 100644
--- a/tools/test/h5jam/getub.c
+++ b/tools/test/h5jam/getub.c
@@ -138,14 +138,15 @@ main(int argc, const char *argv[])
     } /* end if */
 
     /* close things and exit */
+    HDfree(filename);
     HDfree(buf);
     HDclose(fd);
 
     return EXIT_SUCCESS;
 
 error:
-    if (buf)
-        HDfree(buf);
+    HDfree(filename);
+    HDfree(buf);
     if (fd >= 0)
         HDclose(fd);
     return EXIT_FAILURE;
diff --git a/tools/test/h5repack/testfiles/h5repack-help.txt b/tools/test/h5repack/testfiles/h5repack-help.txt
index e12838d..cb10d22 100644
--- a/tools/test/h5repack/testfiles/h5repack-help.txt
+++ b/tools/test/h5repack/testfiles/h5repack-help.txt
@@ -136,6 +136,7 @@ usage: h5repack [OPTIONS] file1 file2
         UD=<filter_number,filter_flag,cd_value_count,value1[,value2,...,valueN]>
             Required values: filter_number, filter_flag, cd_value_count, value1
             Optional values: value2 to valueN
+            filter_flag: 1 is OPTIONAL or 0 is MANDATORY
         NONE (no parameter)
 
     LAYT - is a string with the format:
diff --git a/tools/test/perform/chunk_cache.c b/tools/test/perform/chunk_cache.c
index 3a6a209..1df409c 100644
--- a/tools/test/perform/chunk_cache.c
+++ b/tools/test/perform/chunk_cache.c
@@ -98,7 +98,7 @@ create_dset1(hid_t file)
     hid_t   dcpl             = H5I_INVALID_HID;
     hsize_t dims[RANK]       = {DSET1_DIM1, DSET1_DIM2};
     hsize_t chunk_dims[RANK] = {CHUNK1_DIM1, CHUNK1_DIM2};
-    int **  data; /* data for writing */
+    int **  data             = NULL; /* data for writing */
 
     /* Create the data space. */
     if ((dataspace = H5Screate_simple(RANK, dims, NULL)) < 0)
@@ -134,6 +134,7 @@ create_dset1(hid_t file)
     H5Dclose(dataset);
     H5Pclose(dcpl);
     H5Sclose(dataspace);
+    HDfree(data);
     return 0;
 
 error:
@@ -144,6 +145,7 @@ error:
         H5Sclose(dataspace);
     }
     H5E_END_TRY;
+    HDfree(data);
 
     return 1;
 }
@@ -160,7 +162,7 @@ create_dset2(hid_t file)
     hid_t   dcpl             = H5I_INVALID_HID;
     hsize_t dims[RANK]       = {DSET2_DIM1, DSET2_DIM2};
     hsize_t chunk_dims[RANK] = {CHUNK2_DIM1, CHUNK2_DIM2};
-    int **  data; /* data for writing */
+    int **  data             = NULL; /* data for writing */
 
     /* Create the data space. */
     if ((dataspace = H5Screate_simple(RANK, dims, NULL)) < 0)
@@ -195,6 +197,7 @@ create_dset2(hid_t file)
     H5Dclose(dataset);
     H5Pclose(dcpl);
     H5Sclose(dataspace);
+    HDfree(data);
 
     return 0;
 
@@ -206,6 +209,7 @@ error:
         H5Sclose(dataspace);
     }
     H5E_END_TRY;
+    HDfree(data);
 
     return 1;
 }