1 12 merge java copyright header changes (#391)

* 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

* Whitespace after clang formatting

* Undo format version 11 changes

* Update check to working version

* Merge workflow and minor changes from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge serval small changes from dev

* fix typo

* Minor non-space formatting changes

* GH #386 copyright corrections for java folder

* revert because logic requires false return

4 files changed, 61 insertions, 45 deletions

diff --git a/tools/lib/h5diff_array.c b/tools/lib/h5diff_array.c
index d9616e1..f97ef50 100644
--- a/tools/lib/h5diff_array.c
+++ b/tools/lib/h5diff_array.c
@@ -472,9 +472,7 @@ diff_datum(void *_mem1, void *_mem2, hsize_t elemtno, diff_opt_t *opts, hid_t co
     size_t         size = 0;
     hbool_t        iszero1;
     hbool_t        iszero2;
-    hsize_t        nfound = 0; /* differences found */
-    double         per;
-    hbool_t        both_zero;
+    hsize_t        nfound    = 0; /* differences found */
     diff_err_t     ret_value = opts->err_stat;
 
     H5TOOLS_START_DEBUG("ph:%d elemtno:%d - errstat:%d", opts->print_header, elemtno, opts->err_stat);
@@ -3364,48 +3362,66 @@ print_pos(diff_opt_t *opts, hsize_t idx, size_t u)
             hsize_t curr_pos = idx;
 
             parallel_print("[ ");
-            H5TOOLS_DEBUG("do calc_acc_pos[%ld] nelmts:%d - errstat:%d", i, opts->hs_nelmts, opts->err_stat);
+            H5TOOLS_DEBUG("do calc_acc_pos[%ld] nelmts:%d - errstat:%d", idx, opts->hs_nelmts,
+                          opts->err_stat);
 
             if (opts->sset[0] != NULL) {
                 /* Subsetting is used - calculate total position */
-                hsize_t elmnt_cnt = 1;
-                hsize_t dim_cnt   = 0;   /* previous dim size */
-                hsize_t str_cnt   = 0;   /* previous dim stride */
-                hsize_t curr_idx  = idx; /* calculated running position */
-                hsize_t str_idx   = 0;
-                hsize_t blk_idx   = 0;
-                hsize_t cnt_idx   = 0;
-                hsize_t hs_idx    = 0;
-                j                 = opts->rank - 1;
+                hsize_t prev_dim_size = 0; /* previous dim size */
+                hsize_t prev_str      = 0; /* previouw stride idx*/
+                hsize_t str_cnt       = 0; /* stride multiplier*/
+                hsize_t curr_idx      = 0; /* calculated running position */
+                hsize_t str_idx       = 0;
+                hsize_t blk_idx       = 0;
+                hsize_t cnt_idx       = 0;
+                hsize_t dim_size      = 0; /* current dim size */
+                hsize_t elmnt_cnt     = 1;
+                hsize_t next_idx      = idx;
+                hsize_t data_idx      = 0;
+                j                     = opts->rank - 1;
+                H5TOOLS_DEBUG("...begin:%ld=> opts->rank:%ld (idx:%ld)", j, opts->rank, idx);
                 do {
-                    cnt_idx = opts->sset[0]->count.data[j]; /* Count value for current dim */
-                    H5TOOLS_DEBUG("... sset loop:%d with curr_pos:%ld (curr_idx:%ld) - count:%ld", j,
-                                  curr_pos, curr_idx, cnt_idx);
-                    blk_idx = opts->sset[0]->block.data[j]; /* Block value for current dim */
-                    H5TOOLS_DEBUG("... sset loop:%d with curr_pos:%ld (curr_idx:%ld) - block:%ld", j,
-                                  curr_pos, curr_idx, blk_idx);
-                    hs_idx = cnt_idx * blk_idx; /* hyperslab area value for current dim */
-                    H5TOOLS_DEBUG("... sset loop:%d with curr_pos:%ld (curr_idx:%ld) - hs:%ld", j, curr_pos,
-                                  curr_idx, hs_idx);
-                    str_idx = opts->sset[0]->stride.data[j]; /* Stride value for current dim */
-                    H5TOOLS_DEBUG("... sset loop:%d with curr_pos:%ld (curr_idx:%ld) - stride:%ld", j,
-                                  curr_pos, curr_idx, str_idx);
-                    elmnt_cnt *= opts->dims[j]; /* Total number of elements in dimension */
-                    H5TOOLS_DEBUG("... sset loop:%d with elmnt_cnt:%ld", j, elmnt_cnt);
-                    if (str_idx > blk_idx)
-                        curr_idx += dim_cnt * (str_idx - blk_idx); /* */
-                    else if (curr_idx >= hs_idx)
-                        curr_idx += dim_cnt * str_cnt;
-                    H5TOOLS_DEBUG("... sset loop:%d with idx:%ld (curr_idx:%ld) - stride:%ld", j, idx,
-                                  curr_idx, str_idx);
-                    dim_cnt = elmnt_cnt; /* */
-                    if (str_idx > blk_idx)
-                        str_cnt = str_idx - blk_idx; /* */
-                    else
-                        str_cnt = str_idx; /* */
-                    H5TOOLS_DEBUG("... sset loop:%d with dim_cnt:%ld - str_cnt:%ld", j, dim_cnt, str_cnt);
+                    curr_idx = next_idx;                      /* New current data position */
+                    cnt_idx  = opts->sset[0]->count.data[j];  /* Count value for current dim */
+                    blk_idx  = opts->sset[0]->block.data[j];  /* Block value for current dim */
+                    str_idx  = opts->sset[0]->stride.data[j]; /* Stride value for current dim */
+                    H5TOOLS_DEBUG("... sset loop:%d with curr_pos:%ld (curr_idx:%ld) - c:%ld b:%ld s:%ld", j,
+                                  curr_pos, curr_idx, cnt_idx, blk_idx, str_idx);
+                    dim_size = opts->dims[j]; /* Current dimension size */
+                    // elmnt_cnt *= dim_size;    /* Total number of elements in dimension */
+                    H5TOOLS_DEBUG("... sset loop:%d with elmnt_cnt:%ld - (prev_dim_size:%ld - dim_size:%ld) "
+                                  "- str_cnt:%ld",
+                                  j, elmnt_cnt, prev_dim_size, dim_size, str_cnt);
+                    data_idx = elmnt_cnt * dim_size;
+                    H5TOOLS_DEBUG("... sset loop:%d with curr_pos:%ld (data_idx:%ld)", j, curr_pos, data_idx);
+                    for (i = 0; i < cnt_idx; i++) {
+                        H5TOOLS_DEBUG("... ... data loop:%d with cnt_idx:%ld - str_cnt:%ld (curr_idx:%ld - "
+                                      "data_idx:%ld)",
+                                      i, cnt_idx, str_cnt, curr_idx, data_idx);
+                        if (curr_idx >= data_idx) {
+                            /* get to next block */
+                            data_idx += str_idx * dim_size;
+                            /* get next block */
+                            str_cnt++;
+                            H5TOOLS_DEBUG(
+                                "... ... data loop:%d with cnt_idx:%ld - str_cnt:%ld - data_idx:%ld", i,
+                                cnt_idx, str_cnt, data_idx);
+                        }
+                        H5TOOLS_DEBUG("... ... end data loop:%d with dim_cnt:%ld - str_cnt:%ld - "
+                                      "(curr_idx:%ld - data_idx:%ld)",
+                                      i, dim_size, str_cnt, curr_idx, data_idx);
+                    }
+                    next_idx += dim_size * str_cnt; // + prev_dim_size;
+                    H5TOOLS_DEBUG("... sset loop:%d with curr_idx:%ld (next_idx:%ld)", j, curr_idx, next_idx);
+                    str_cnt       = 0;
+                    prev_str      = str_idx;
+                    prev_dim_size = dim_size;
+                    H5TOOLS_DEBUG("... end sset loop:%d with prev_dim_size:%ld (curr_idx:%ld - data_idx:%ld) "
+                                  "- str_cnt:%ld",
+                                  j, prev_dim_size, curr_idx, data_idx, str_cnt);
+                    elmnt_cnt *= dim_size; /* Total number of elements in dimension */
                     j--;
-                } while (curr_idx >= elmnt_cnt && j >= 0);
+                } while (next_idx >= elmnt_cnt && j >= 0);
                 curr_pos = curr_idx; /* New current position */
                 H5TOOLS_DEBUG("pos loop:%d,%d with  elmnt_cnt:%ld - curr_pos:%ld", i, j, elmnt_cnt, curr_pos);
             } /* if (opts->sset[0] != NULL) */
diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c
index f6566d9..3b78491 100644
--- a/tools/lib/h5tools.c
+++ b/tools/lib/h5tools.c
@@ -1778,7 +1778,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
         } break;
         case H5T_ARRAY: {
             int     k, ndims;
-            hsize_t dims[H5S_MAX_RANK], temp_nelmts, nelmts;
+            hsize_t dims[H5S_MAX_RANK], temp_nelmts, nelmts = 0;
             hid_t   memb = H5I_INVALID_HID;
 
             H5TOOLS_DEBUG("H5T_ARRAY");
diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c
index dd3ae67..212b13e 100644
--- a/tools/lib/h5tools_str.c
+++ b/tools/lib/h5tools_str.c
@@ -705,7 +705,7 @@ h5tools_str_sprint(h5tools_str_t *str, const h5tool_format_t *info, hid_t contai
                     long double templdouble;
 
                     HDmemcpy(&templdouble, vp, sizeof(long double));
-                    h5tools_str_append(str, OPT(info->fmt_double, "%Lf"), templdouble);
+                    h5tools_str_append(str, "%Lg", templdouble);
 #endif
                 }
                 break;
diff --git a/tools/lib/h5tools_utils.c b/tools/lib/h5tools_utils.c
index 708fb2c..b33d908 100644
--- a/tools/lib/h5tools_utils.c
+++ b/tools/lib/h5tools_utils.c
@@ -196,7 +196,7 @@ get_option(int argc, const char **argv, const char *opts, const struct long_opti
         /* long command line option */
         int        i;
         const char ch      = '=';
-        char *     arg     = &argv[opt_ind][2];
+        char *     arg     = HDstrdup(&argv[opt_ind][2]);
         size_t     arg_len = 0;
 
         opt_arg = strchr(&argv[opt_ind][2], ch);
@@ -208,8 +208,6 @@ get_option(int argc, const char **argv, const char *opts, const struct long_opti
         arg[arg_len] = 0;
 
         for (i = 0; l_opts && l_opts[i].name; i++) {
-            size_t len = HDstrlen(l_opts[i].name);
-
             if (HDstrcmp(arg, l_opts[i].name) == 0) {
                 /* we've found a matching long command line flag */
                 opt_opt = l_opts[i].shortval;
@@ -253,6 +251,8 @@ get_option(int argc, const char **argv, const char *opts, const struct long_opti
 
         opt_ind++;
         sp = 1;
+
+        HDfree(arg);
     }
     else {
         register char *cp; /* pointer into current token */