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

7 files changed, 34 insertions, 28 deletions

diff --git a/tools/src/h5diff/h5diff_common.c b/tools/src/h5diff/h5diff_common.c
index b51950e..99cd653 100644
--- a/tools/src/h5diff/h5diff_common.c
+++ b/tools/src/h5diff/h5diff_common.c
@@ -76,7 +76,6 @@ check_options(diff_opt_t *opts)
     }
 }
 
-#if TRILABS_227
 /*-------------------------------------------------------------------------
  * Function:    parse_hsize_list
  *
@@ -192,7 +191,6 @@ parse_subset_params(const char *dset)
 
     return s;
 }
-#endif
 
 /*-------------------------------------------------------------------------
  * Function: parse_command_line
@@ -480,11 +478,9 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
      * TRILABS_227 is complete except for an issue with printing indices
      * the following calls will enable subsetting
      */
-#if TRILABS_227
     opts->sset[0] = parse_subset_params(*objname1);
 
     opts->sset[1] = parse_subset_params(*objname2);
-#endif
 
     H5TOOLS_ENDDEBUG("");
 }
@@ -822,19 +818,27 @@ usage(void)
     /*
      * TRILABS_227 is complete except for an issue with printing indices
      * the following will be needed for subsetting
+     */
     PRINTVALSTREAM(rawoutstream, " Subsetting options:\n");
-    PRINTVALSTREAM(rawoutstream, "  Subsetting is available by using the fcompact form of subsetting, as
-    follows:\n"); PRINTVALSTREAM(rawoutstream, "    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]\n");
-    PRINTVALSTREAM(rawoutstream, "  It is not required to use all parameters, but until the last parameter
-    value used,\n"); PRINTVALSTREAM(rawoutstream, "  all of the semicolons (;) are required, even when a
-    parameter value is not specified. Example:\n"); PRINTVALSTREAM(rawoutstream, "    obj1
-    /foo/mydataset[START;;COUNT;BLOCK]\n"); PRINTVALSTREAM(rawoutstream, "    obj1 /foo/mydataset[START]\n");
-    PRINTVALSTREAM(rawoutstream, "  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1
-    in\n"); PRINTVALSTREAM(rawoutstream, "  each dimension. START is optional and will default to 0 in each
-    dimension.\n"); PRINTVALSTREAM(rawoutstream, "  Each of START, STRIDE, COUNT, and BLOCK must be a
-    comma-separated list of integers with\n"); PRINTVALSTREAM(rawoutstream, "  one integer for each dimension
-    of the dataset.\n"); PRINTVALSTREAM(rawoutstream, "\n");
-   */
+    PRINTVALSTREAM(rawoutstream,
+                   "  Subsetting is available by using the fcompact form of subsetting, as follows:\n");
+    PRINTVALSTREAM(rawoutstream, "    obj1 /foo/mydataset[START;STRIDE;COUNT;BLOCK]\n");
+    PRINTVALSTREAM(rawoutstream,
+                   "  It is not required to use all parameters, but until the last parameter value used,\n");
+    PRINTVALSTREAM(
+        rawoutstream,
+        "  all of the semicolons (;) are required, even when a parameter value is not specified. Example:\n");
+    PRINTVALSTREAM(rawoutstream, "    obj1 /foo/mydataset[START;;COUNT;BLOCK]\n");
+    PRINTVALSTREAM(rawoutstream, "    obj1 /foo/mydataset[START]\n");
+    PRINTVALSTREAM(rawoutstream,
+                   "  The STRIDE, COUNT, and BLOCK parameters are optional and will default to 1 in\n");
+    PRINTVALSTREAM(rawoutstream,
+                   "  each dimension. START is optional and will default to 0 in each dimension.\n");
+    PRINTVALSTREAM(
+        rawoutstream,
+        "  Each of START, STRIDE, COUNT, and BLOCK must be a comma-separated list of integers with\n");
+    PRINTVALSTREAM(rawoutstream, "  one integer for each dimension of the dataset.\n");
+    PRINTVALSTREAM(rawoutstream, "\n");
     PRINTVALSTREAM(rawoutstream, " Exit code:\n");
     PRINTVALSTREAM(rawoutstream, "  0 if no differences, 1 if differences found, 2 if error\n");
     PRINTVALSTREAM(rawoutstream, "\n");
diff --git a/tools/src/h5import/h5import.c b/tools/src/h5import/h5import.c
index e3f4384..471af51 100644
--- a/tools/src/h5import/h5import.c
+++ b/tools/src/h5import/h5import.c
@@ -2536,7 +2536,7 @@ parsePathInfo(struct path_info *path, char *temp)
 
     token = HDstrtok(temp, delimiter);
     if (HDstrlen(token) >= MAX_PATH_NAME_LENGTH) {
-        (void)HDfprintf(stderr, err1);
+        (void)HDfprintf(stderr, "%s", err1);
         return (-1);
     }
     HDstrcpy(path->group[i++], token);
@@ -2546,7 +2546,7 @@ parsePathInfo(struct path_info *path, char *temp)
         if (token == NULL)
             break;
         if (HDstrlen(token) >= MAX_PATH_NAME_LENGTH) {
-            (void)HDfprintf(stderr, err1);
+            (void)HDfprintf(stderr, "%s", err1);
             return (-1);
         }
         HDstrcpy(path->group[i++], token);
diff --git a/tools/src/h5ls/h5ls.c b/tools/src/h5ls/h5ls.c
index b29ed72..06c90d0 100644
--- a/tools/src/h5ls/h5ls.c
+++ b/tools/src/h5ls/h5ls.c
@@ -2648,7 +2648,7 @@ int
 main(int argc, const char *argv[])
 {
     hid_t              file_id = H5I_INVALID_HID;
-    char *             fname = NULL, *oname = NULL, *x;
+    char *             fname = NULL, *oname = NULL, *x = NULL;
     const char *       s = NULL;
     char *             rest;
     int                argno;
diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c
index 20d277d..0aef710 100644
--- a/tools/src/h5repack/h5repack_copy.c
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -357,14 +357,14 @@ copy_objects(const char *fnamein, const char *fnameout, pack_opt_t *options)
 done:
     H5E_BEGIN_TRY
     {
-        H5Pclose(fcpl_in);
-        H5Pclose(gcpl_in);
         H5Pclose(fcpl);
+        H5Pclose(options->fout_fapl);
+        options->fout_fapl = H5P_DEFAULT;
+        H5Pclose(gcpl_in);
         H5Gclose(grp_in);
-        H5Fclose(fidin);
+        H5Pclose(fcpl_in);
         H5Fclose(fidout);
         H5Fclose(fidin);
-        H5Fclose(fidout);
     }
     H5E_END_TRY;
     if (travt)
diff --git a/tools/src/h5repack/h5repack_verify.c b/tools/src/h5repack/h5repack_verify.c
index cc5501d..0542d03 100644
--- a/tools/src/h5repack/h5repack_verify.c
+++ b/tools/src/h5repack/h5repack_verify.c
@@ -378,9 +378,11 @@ h5repack_cmp_pl(const char *fname1, hid_t fname1_fapl, const char *fname2, hid_t
      *-------------------------------------------------------------------------
      */
     /* Open the files */
-    if ((fid1 = h5tools_fopen(fname1, H5F_ACC_RDONLY, fname1_fapl, TRUE, NULL, 0)) < 0)
+    if ((fid1 = h5tools_fopen(fname1, H5F_ACC_RDONLY, fname1_fapl,
+                              (fname1_fapl == H5P_DEFAULT) ? FALSE : TRUE, NULL, 0)) < 0)
         H5TOOLS_GOTO_ERROR((-1), "h5tools_fopen failed <%s>: %s", fname1, H5FOPENERROR);
-    if ((fid2 = h5tools_fopen(fname2, H5F_ACC_RDONLY, fname2_fapl, TRUE, NULL, 0)) < 0)
+    if ((fid2 = h5tools_fopen(fname2, H5F_ACC_RDONLY, fname2_fapl,
+                              (fname2_fapl == H5P_DEFAULT) ? FALSE : TRUE, NULL, 0)) < 0)
         H5TOOLS_GOTO_ERROR((-1), "h5tools_fopen failed <%s>: %s", fname2, H5FOPENERROR);
 
     /*-------------------------------------------------------------------------
diff --git a/tools/src/misc/h5debug.c b/tools/src/misc/h5debug.c
index 2426a11..8962a76 100644
--- a/tools/src/misc/h5debug.c
+++ b/tools/src/misc/h5debug.c
@@ -246,8 +246,8 @@ main(int argc, char *argv[])
     haddr_t        extra[10];
     uint8_t        sig[H5F_SIGNATURE_LEN];
     size_t         u;
-    H5E_auto2_t    func;
-    void *         edata;
+    H5E_auto2_t    func           = NULL;
+    void *         edata          = NULL;
     hbool_t        api_ctx_pushed = FALSE; /* Whether API context pushed */
     herr_t         status         = SUCCEED;
     int            exit_value     = 0;
diff --git a/tools/src/misc/h5repart.c b/tools/src/misc/h5repart.c
index 77b40a1..a75f6d8 100644
--- a/tools/src/misc/h5repart.c
+++ b/tools/src/misc/h5repart.c
@@ -97,7 +97,7 @@ static off_t
 get_size(const char *progname, int *argno, int argc, char *argv[])
 {
     off_t retval = -1;
-    char *suffix;
+    char *suffix = NULL;
 
     if (isdigit((int)(argv[*argno][2]))) {
         retval = HDstrtol(argv[*argno] + 2, &suffix, 10);