Primary change is HDFFV-11212 - new refs and JNI (#372)

* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* OESS-98 fix tools test for plugins

* Keep doxygen comments under 100 chars long - format hint

* Whitespace

* HDFFV-11144 - Reclassify CMake messages

* HDFFV-11099/11100 added help text

* Reworked switch statement to compare string instead

* Fix typo

* Update CDash mode

* Correct name of threadsafe

* Correct option name

* Undo accidental commit

* Note LLVM 10 to 11 format default changes

* Update format plugin

* Undo clang-format version 11 changes

* One more correction

* Update supported platforms

* Revert whitespace changes

* Correct whitespace

* Changes from PR#3

* HDFFV-11213 added option to control gcc10 warnings diagnostics

* HDFFV-11212 Use the new references correctly in JNI utility and tests

* format source

* Fix typo

* Add new test file

* HDFFV-11212 - update test and remove unused arg

* Minor non-space formatting changes

* Use H5I_INVALID_ID instead of "-1"

* source formatting

* add missing testfile, update jni function

* Undo commit of debug code

* remove mislocated file

* Fix h5repack test for handling of fapls and id close

* Update h5diff test files usage text

* HDFFV-11212 add new ref tests for JNI export dataset

* src format update

* Remove blank line typo

* src format typo

* long double requires %Lg

* Another long double foramt specifer S.B. %Lg

* issue with t128bit test

* Windows issue with h5dump and type.

* Fix review issues

* refactor function nesting and fix error checks

* format fixes

* Remove untested functions and javadoc quiet comments

* Restore TRY block.

* Change string append errors to memory exception

* revert to H5_JNI_FATAL_ERROR - support functions need work

* Add assertion error for h5util functions

* remove duplicate function

* format fix

* Revert HD function error handling

* Update copyright comments

3 files changed, 28 insertions, 22 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/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);
 
     /*-------------------------------------------------------------------------