1 10 Merges from develop (#424)

* HDFFV-10865 - merge from dev, HDFArray perf fix.

* Remove duplicate setting

* Whitespace changes after clang format

* Undo version 11 clang format changes

* Merge CMake changes from develop

* test testing script merge from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge small changes from develop

* Minor non-space formatting changes

* #386 copyright corrections for java folder

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Merge updates

#358 patches from vtk
#361 fix header guard spelling

* format fix

* Fix missing underscore and make H5public.h closer to dev

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
header guard underscore cleanup
JNI cleanup

* format alignment

* Add missing test ref file

13 files changed, 50 insertions, 46 deletions

diff --git a/tools/src/h5diff/h5diff_common.c b/tools/src/h5diff/h5diff_common.c
index 471400f..6402384 100644
--- a/tools/src/h5diff/h5diff_common.c
+++ b/tools/src/h5diff/h5diff_common.c
@@ -70,7 +70,6 @@ check_options(diff_opt_t *opts)
     }
 }
 
-#if TRILABS_227
 /*-------------------------------------------------------------------------
  * Function:    parse_hsize_list
  *
@@ -186,7 +185,6 @@ parse_subset_params(const char *dset)
 
     return s;
 }
-#endif
 
 /*-------------------------------------------------------------------------
  * Function: parse_command_line
@@ -442,11 +440,9 @@ 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("");
 }
@@ -766,19 +762,27 @@ 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/h5diff/h5diff_common.h b/tools/src/h5diff/h5diff_common.h
index 6594478..83f4255 100644
--- a/tools/src/h5diff/h5diff_common.h
+++ b/tools/src/h5diff/h5diff_common.h
@@ -11,8 +11,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef H5DIFFCOMMON_H__
-#define H5DIFFCOMMON_H__
+#ifndef H5DIFFCOMMON_H
+#define H5DIFFCOMMON_H
 
 #include "h5tools.h"
 /* Name of tool */
@@ -32,4 +32,4 @@ void print_info(diff_opt_t *opts);
 }
 #endif
 
-#endif /* H5DIFFCOMMON_H__ */
+#endif /* H5DIFFCOMMON_H */
diff --git a/tools/src/h5dump/h5dump.h b/tools/src/h5dump/h5dump.h
index 60422ad..a53d1ba 100644
--- a/tools/src/h5dump/h5dump.h
+++ b/tools/src/h5dump/h5dump.h
@@ -10,8 +10,8 @@
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
-#ifndef H5DUMP_H__
-#define H5DUMP_H__
+#ifndef H5DUMP_H
+#define H5DUMP_H
 
 #include "hdf5.h"
 #include "H5private.h"
@@ -112,4 +112,4 @@ const dump_functions *dump_function_table;
 }
 #endif
 
-#endif /* !H5DUMP_H__ */
+#endif /* H5DUMP_H */
diff --git a/tools/src/h5dump/h5dump_ddl.h b/tools/src/h5dump/h5dump_ddl.h
index 6d65796..8487270 100644
--- a/tools/src/h5dump/h5dump_ddl.h
+++ b/tools/src/h5dump/h5dump_ddl.h
@@ -11,8 +11,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef H5DUMP_DDL_H__
-#define H5DUMP_DDL_H__
+#ifndef H5DUMP_DDL_H
+#define H5DUMP_DDL_H
 
 #ifdef __cplusplus
 extern "C" {
@@ -50,4 +50,4 @@ void handle_datatypes(hid_t fid, const char *type, void H5_ATTR_UNUSED *data, in
 }
 #endif
 
-#endif /* !H5DUMP_DDL_H__ */
+#endif /* H5DUMP_DDL_H */
diff --git a/tools/src/h5dump/h5dump_defines.h b/tools/src/h5dump/h5dump_defines.h
index 0fb8def..21a31dd 100644
--- a/tools/src/h5dump/h5dump_defines.h
+++ b/tools/src/h5dump/h5dump_defines.h
@@ -10,8 +10,8 @@
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
-#ifndef H5DUMP_DEFINES_H__
-#define H5DUMP_DEFINES_H__
+#ifndef H5DUMP_DEFINES_H
+#define H5DUMP_DEFINES_H
 
 #define H5DUMP_MAX_RANK H5S_MAX_RANK
 
@@ -50,4 +50,4 @@
 #define H5_SZIP_MSB_OPTION_MASK 16
 #define H5_SZIP_RAW_OPTION_MASK 128
 
-#endif /* !H5DUMP_DEFINES_H__ */
+#endif /* H5DUMP_DEFINES_H */
diff --git a/tools/src/h5dump/h5dump_extern.h b/tools/src/h5dump/h5dump_extern.h
index 8fbb5af..308f602 100644
--- a/tools/src/h5dump/h5dump_extern.h
+++ b/tools/src/h5dump/h5dump_extern.h
@@ -10,8 +10,8 @@
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
-#ifndef H5DUMP_EXTERN_H__
-#define H5DUMP_EXTERN_H__
+#ifndef H5DUMP_EXTERN_H
+#define H5DUMP_EXTERN_H
 
 #include "hdf5.h"
 #include "H5private.h"
@@ -109,4 +109,4 @@ ssize_t table_list_visited(unsigned long file_no);
 }
 #endif
 
-#endif /* !H5DUMP_EXTERN_H__ */
+#endif /* H5DUMP_EXTERN_H */
diff --git a/tools/src/h5dump/h5dump_xml.h b/tools/src/h5dump/h5dump_xml.h
index 9ff22ed..d69f6d5 100644
--- a/tools/src/h5dump/h5dump_xml.h
+++ b/tools/src/h5dump/h5dump_xml.h
@@ -10,8 +10,8 @@
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
-#ifndef H5DUMP_XML_H__
-#define H5DUMP_XML_H__
+#ifndef H5DUMP_XML_H
+#define H5DUMP_XML_H
 
 extern const char *xmlnsprefix;
 
@@ -34,4 +34,4 @@ void   xml_dump_data(hid_t, int, struct subset_t *, int);
 }
 #endif
 
-#endif /* !H5DUMP_XML_H__ */
+#endif /* H5DUMP_XML_H */
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/h5import/h5import.h b/tools/src/h5import/h5import.h
index 2192f4a..efd40e1 100644
--- a/tools/src/h5import/h5import.h
+++ b/tools/src/h5import/h5import.h
@@ -17,8 +17,8 @@
  *
  */
 
-#ifndef H5IMPORT_H__
-#define H5IMPORT_H__
+#ifndef H5IMPORT_H
+#define H5IMPORT_H
 
 /*
  * state table tokens
@@ -189,4 +189,4 @@ void help(char *);
 hid_t createOutputDataType(struct Input *in);
 hid_t createInputDataType(struct Input *in);
 
-#endif /* H5IMPORT_H__ */
+#endif /* H5IMPORT_H */
diff --git a/tools/src/h5ls/h5ls.c b/tools/src/h5ls/h5ls.c
index 23cde21..1f9c681 100644
--- a/tools/src/h5ls/h5ls.c
+++ b/tools/src/h5ls/h5ls.c
@@ -2622,7 +2622,7 @@ 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.h b/tools/src/h5repack/h5repack.h
index f022934..ca1269b 100644
--- a/tools/src/h5repack/h5repack.h
+++ b/tools/src/h5repack/h5repack.h
@@ -11,8 +11,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef H5REPACK_H__
-#define H5REPACK_H__
+#ifndef H5REPACK_H
+#define H5REPACK_H
 
 #include "H5private.h"
 #include "hdf5.h"
@@ -224,4 +224,4 @@ obj_list_t *parse_filter(const char *str, unsigned *n_objs, filter_info_t *filt,
 obj_list_t *parse_layout(const char *str, unsigned *n_objs, pack_info_t *pack, /* info about object */
                          pack_opt_t *options);
 
-#endif /* H5REPACK_H__ */
+#endif /* H5REPACK_H */
diff --git a/tools/src/misc/h5debug.c b/tools/src/misc/h5debug.c
index e8e7f29..88a3462 100644
--- a/tools/src/misc/h5debug.c
+++ b/tools/src/misc/h5debug.c
@@ -245,8 +245,8 @@ 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);