Hdf5 merge issue 458 v110 (#465)

* close #195. (#196)

* Update HDF5PluginMacros.cmake

* Update HDF5PluginMacros.cmake

* Modify temporary rpath for testing in java example scripts. (#230)

* Fix undefined left shifting of negative numbers (#338)

Undefined Bahavior Sanitizer errored here about left shifting negative numbers.

* Update license url (#332)

* Modify temporary rpath for testing in java example scripts.

* Update URL in source file Copyright headers for web copy of COPYING
file - src and test directories.

* Applied clang-tidy readability-non-const-parameter warning fixes auto… (#429)

* Automatically applied clang-tidy readability-avoid-const-params-in-decls fixes

Removes useless const declarations.

* Fixed most readability-non-const-parameter warnings

These changes were made automatically by clang-tidy, but I manually reverted the changes related to the H5Z_func_t signature.

* Reformat source with clang v10.0.1.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

* Added C++11 override keyword where appropriate (#433)

Added H5_OVERRIDE macro for compatibility with both C++11 and older.

* Various clang tidy warning fixes (#448)

* Fixed clang-tidy bugprone-reserved-identifier warnings

* Fixed clang-tidy bugprone-assert-side-effect warnings

* Fixed clang-tidy bugprone-copy-constructor-init warning

* Fixed clang-tidy readability-redundant-preprocessor warning

For error_test.c the removed code was already dead, because it was in the else of an `#if H5_USE_16_API` block.

Based on H5Location.h, I think p_get_ref_obj_type was meant to be in `#ifndef DOXYGEN_SHOULD_SKIP_THIS` and an `#endif` was missing.  Similarly, in the header, getObjTypeByIdx is only in H5_NO_DEPRECATED_SYMBOLS, not DOXYGEN_SHOULD_SKIP_THIS.

* Fixed clang-tidy readability-redundant-string-init warnings

* Fixed some clang-tidy performance-type-promotion-in-math-fn warnings

* Fixed clang-tidy performance-unnecessary-value-param warnings

* Reformat source with clang v10.0.1.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

* Removed checks/workarounds for pre-C++89 compatibility (#449)

After 30+ years, just assume that the following exist:
- extension-less includes
- namespaces
- std::
- static_cast
- bool

* Fixed all clang-tidy bugprone-suspicious-string-compare warnings (#451)

* Fixed all clang-tidy bugprone-suspicious-string-compare warnings

This change was generated entirely by clang-tidy itself.

* Reformat code with clang v10.0.1.

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

* Fix clang-tidy suspicious string compare in H5A.c missed in merge.

Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Sean McBride <sean@rogue-research.com>

10 files changed, 29 insertions, 27 deletions

diff --git a/tools/lib/h5diff.c b/tools/lib/h5diff.c
index ce505a3..d55b605 100644
--- a/tools/lib/h5diff.c
+++ b/tools/lib/h5diff.c
@@ -660,7 +660,7 @@ h5diff(const char *fname1, const char *fname2, const char *objname1, const char
     /* if any object is specified */
     if (objname1) {
         /* make the given object1 fullpath, start with "/"  */
-        if (HDstrncmp(objname1, "/", 1)) {
+        if (HDstrncmp(objname1, "/", 1) != 0) {
 #ifdef H5_HAVE_ASPRINTF
             /* Use the asprintf() routine, since it does what we're trying to do below */
             if (HDasprintf(&obj1fullname, "/%s", objname1) < 0)
@@ -679,7 +679,7 @@ h5diff(const char *fname1, const char *fname2, const char *objname1, const char
         H5TOOLS_DEBUG("obj1fullname = %s", obj1fullname);
 
         /* make the given object2 fullpath, start with "/" */
-        if (HDstrncmp(objname2, "/", 1)) {
+        if (HDstrncmp(objname2, "/", 1) != 0) {
 #ifdef H5_HAVE_ASPRINTF
             /* Use the asprintf() routine, since it does what we're trying to do below */
             if (HDasprintf(&obj2fullname, "/%s", objname2) < 0)
@@ -986,7 +986,7 @@ h5diff(const char *fname1, const char *fname2, const char *objname1, const char
 
             parallel_print("\n");
             /* if given objects is group under root */
-            if (HDstrcmp(obj1fullname, "/") || HDstrcmp(obj2fullname, "/"))
+            if (HDstrcmp(obj1fullname, "/") != 0 || HDstrcmp(obj2fullname, "/") != 0)
                 parallel_print("group1   group2\n");
             else
                 parallel_print("file1     file2\n");
@@ -1084,9 +1084,9 @@ diff_match(hid_t file1_id, const char *grp1, trav_info_t *info1, hid_t file2_id,
      * if not root, prepare object name to be pre-appended to group path to
      * make full path
      */
-    if (HDstrcmp(grp1, "/"))
+    if (HDstrcmp(grp1, "/") != 0)
         grp1_path = grp1;
-    if (HDstrcmp(grp2, "/"))
+    if (HDstrcmp(grp2, "/") != 0)
         grp2_path = grp2;
 
     /*-------------------------------------------------------------------------
diff --git a/tools/lib/h5diff_attr.c b/tools/lib/h5diff_attr.c
index 8283579..642b57b 100644
--- a/tools/lib/h5diff_attr.c
+++ b/tools/lib/h5diff_attr.c
@@ -104,7 +104,7 @@ table_attrs_free(table_attrs_t *table)
  * Date: March 15, 2011
  *------------------------------------------------------------------------*/
 static void
-table_attr_mark_exist(unsigned *exist, char *name, table_attrs_t *table)
+table_attr_mark_exist(const unsigned *exist, char *name, table_attrs_t *table)
 {
     if (table->nattrs == table->size) {
         match_attr_t *new_attrs;
diff --git a/tools/lib/h5tools.c b/tools/lib/h5tools.c
index baaf665..a6847d4 100644
--- a/tools/lib/h5tools.c
+++ b/tools/lib/h5tools.c
@@ -1430,7 +1430,7 @@ h5tools_render_region_element(FILE *stream, const h5tool_format_t *info, h5tools
  *-------------------------------------------------------------------------
  */
 void
-init_acc_pos(unsigned ndims, hsize_t *dims, hsize_t *acc, hsize_t *pos, hsize_t *p_min_idx)
+init_acc_pos(unsigned ndims, const hsize_t *dims, hsize_t *acc, hsize_t *pos, hsize_t *p_min_idx)
 {
     int      i;
     unsigned j;
@@ -1463,7 +1463,7 @@ init_acc_pos(unsigned ndims, hsize_t *dims, hsize_t *acc, hsize_t *pos, hsize_t
  *-------------------------------------------------------------------------
  */
 hsize_t
-calc_acc_pos(unsigned ndims, hsize_t elmtno, hsize_t *acc, hsize_t *pos)
+calc_acc_pos(unsigned ndims, hsize_t elmtno, const hsize_t *acc, hsize_t *pos)
 {
     int     i;
     hsize_t curr_pos = elmtno;
@@ -1731,7 +1731,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
  */
 int
 render_bin_output_region_data_blocks(hid_t region_id, FILE *stream, hid_t container, unsigned ndims,
-                                     hid_t type_id, hsize_t nblocks, hsize_t *ptdata)
+                                     hid_t type_id, hsize_t nblocks, const hsize_t *ptdata)
 {
     hsize_t *dims1 = NULL;
     hsize_t *start = NULL;
@@ -2039,12 +2039,12 @@ h5tools_is_obj_same(hid_t loc_id1, const char *name1, hid_t loc_id2, const char
     H5O_info_t oinfo1, oinfo2;
     hbool_t    ret_val = FALSE;
 
-    if (name1 && HDstrcmp(name1, "."))
+    if (name1 && HDstrcmp(name1, ".") != 0)
         H5Oget_info_by_name2(loc_id1, name1, &oinfo1, H5O_INFO_BASIC, H5P_DEFAULT);
     else
         H5Oget_info2(loc_id1, &oinfo1, H5O_INFO_BASIC);
 
-    if (name2 && HDstrcmp(name2, "."))
+    if (name2 && HDstrcmp(name2, ".") != 0)
         H5Oget_info_by_name2(loc_id2, name2, &oinfo2, H5O_INFO_BASIC, H5P_DEFAULT);
     else
         H5Oget_info2(loc_id2, &oinfo2, H5O_INFO_BASIC);
diff --git a/tools/lib/h5tools.h b/tools/lib/h5tools.h
index 53f16cf..d75506d 100644
--- a/tools/lib/h5tools.h
+++ b/tools/lib/h5tools.h
@@ -648,8 +648,9 @@ H5TOOLS_DLL hid_t   h5tools_get_big_endian_type(hid_t type);
 H5TOOLS_DLL htri_t  h5tools_detect_vlen(hid_t tid);
 H5TOOLS_DLL htri_t  h5tools_detect_vlen_str(hid_t tid);
 H5TOOLS_DLL hbool_t h5tools_is_obj_same(hid_t loc_id1, const char *name1, hid_t loc_id2, const char *name2);
-H5TOOLS_DLL void init_acc_pos(unsigned ndims, hsize_t *dims, hsize_t *acc, hsize_t *pos, hsize_t *p_min_idx);
-H5TOOLS_DLL hsize_t calc_acc_pos(unsigned ndims, hsize_t elemtno, hsize_t *acc, hsize_t *pos);
+H5TOOLS_DLL void    init_acc_pos(unsigned ndims, const hsize_t *dims, hsize_t *acc, hsize_t *pos,
+                                 hsize_t *p_min_idx);
+H5TOOLS_DLL hsize_t calc_acc_pos(unsigned ndims, hsize_t elemtno, const hsize_t *acc, hsize_t *pos);
 H5TOOLS_DLL hbool_t h5tools_is_zero(const void *_mem, size_t size);
 H5TOOLS_DLL int     h5tools_canreadf(const char *name, hid_t dcpl_id);
 H5TOOLS_DLL int     h5tools_can_encode(H5Z_filter_t filtn);
@@ -663,7 +664,7 @@ H5TOOLS_DLL void h5tools_region_simple_prefix(FILE *stream, const h5tool_format_
 H5TOOLS_DLL int     render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t nelmts);
 H5TOOLS_DLL int     render_bin_output_region_data_blocks(hid_t region_id, FILE *stream, hid_t container,
                                                          unsigned ndims, hid_t type_id, hsize_t nblocks,
-                                                         hsize_t *ptdata);
+                                                         const hsize_t *ptdata);
 H5TOOLS_DLL hbool_t render_bin_output_region_blocks(hid_t region_space, hid_t region_id, FILE *stream,
                                                     hid_t container);
 H5TOOLS_DLL int     render_bin_output_region_data_points(hid_t region_space, hid_t region_id, FILE *stream,
diff --git a/tools/lib/h5tools_dump.c b/tools/lib/h5tools_dump.c
index 9b647b2..caecfda 100644
--- a/tools/lib/h5tools_dump.c
+++ b/tools/lib/h5tools_dump.c
@@ -1257,12 +1257,12 @@ done:
 static herr_t
 h5tools_print_simple_subset(FILE *stream, const h5tool_format_t *info, h5tools_context_t *ctx, hid_t dset,
                             hid_t p_type, hid_t f_space, hsize_t hyperslab_count,
-                            hsize_t *    temp_start,  /* start inside offset count loop */
-                            hsize_t *    temp_count,  /* count inside offset count loop  */
-                            hsize_t *    temp_block,  /* block size used in loop  */
-                            hsize_t *    temp_stride, /* stride size used in loop  */
-                            hsize_t *    total_size,  /* total size of dataset */
-                            unsigned int row_dim)     /* index of row_counter dimension */
+                            hsize_t *      temp_start,  /* start inside offset count loop */
+                            hsize_t *      temp_count,  /* count inside offset count loop  */
+                            hsize_t *      temp_block,  /* block size used in loop  */
+                            hsize_t *      temp_stride, /* stride size used in loop  */
+                            const hsize_t *total_size,  /* total size of dataset */
+                            unsigned int   row_dim)       /* index of row_counter dimension */
 {
     size_t         i;                          /* counters  */
     size_t         j;                          /* counters  */
diff --git a/tools/lib/h5tools_ref.c b/tools/lib/h5tools_ref.c
index ff975e3..2adec9f 100644
--- a/tools/lib/h5tools_ref.c
+++ b/tools/lib/h5tools_ref.c
@@ -169,7 +169,7 @@ ref_path_table_lookup(const char *thepath)
     if ((thepath == NULL) || (HDstrlen(thepath) == 0))
         return HADDR_UNDEF;
     /* Allow lookups on the root group, even though it doesn't have any link info */
-    if (HDstrcmp(thepath, "/")) {
+    if (HDstrcmp(thepath, "/") != 0) {
         H5L_info_t li;
 
         /* Check for external link first, so we don't return the OID of an object in another file */
diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c
index 41a12d7..0597423 100644
--- a/tools/lib/h5tools_str.c
+++ b/tools/lib/h5tools_str.c
@@ -142,7 +142,7 @@ h5tools_str_append(h5tools_str_t *str /*in,out*/, const char *fmt, ...)
             /* failure, such as bad format */
             return NULL;
 
-        if ((size_t)nchars >= avail || (0 == nchars && (HDstrcmp(fmt, "%s")))) {
+        if ((size_t)nchars >= avail || (0 == nchars && (HDstrcmp(fmt, "%s") != 0))) {
             /* Truncation return value as documented by C99, or zero return value with either of the
              * following conditions, each of which indicates that the proper C99 return value probably
              *  should have been positive when the format string is
@@ -323,7 +323,7 @@ h5tools_str_prefix(h5tools_str_t *str /*in,out*/, const h5tool_format_t *info, h
  */
 char *
 h5tools_str_region_prefix(h5tools_str_t *str /*in,out*/, const h5tool_format_t *info, hsize_t elmtno,
-                          hsize_t *ptdata, h5tools_context_t *ctx)
+                          const hsize_t *ptdata, h5tools_context_t *ctx)
 {
     size_t i = 0;
 
diff --git a/tools/lib/h5tools_str.h b/tools/lib/h5tools_str.h
index 3bbf6b1..ad43590 100644
--- a/tools/lib/h5tools_str.h
+++ b/tools/lib/h5tools_str.h
@@ -36,7 +36,7 @@ H5TOOLS_DLL char * h5tools_str_prefix(h5tools_str_t *str, const h5tool_format_t
  * new functions needed to display region reference data
  */
 H5TOOLS_DLL char *h5tools_str_region_prefix(h5tools_str_t *str, const h5tool_format_t *info, hsize_t elmtno,
-                                            hsize_t *ptdata, h5tools_context_t *ctx);
+                                            const hsize_t *ptdata, h5tools_context_t *ctx);
 H5TOOLS_DLL void  h5tools_str_dump_space_slabs(h5tools_str_t *, hid_t, const h5tool_format_t *,
                                                h5tools_context_t *ctx);
 H5TOOLS_DLL void  h5tools_str_dump_space_blocks(h5tools_str_t *, hid_t, const h5tool_format_t *);
diff --git a/tools/lib/h5trav.c b/tools/lib/h5trav.c
index 58e4b35..dd30cb5 100644
--- a/tools/lib/h5trav.c
+++ b/tools/lib/h5trav.c
@@ -351,7 +351,7 @@ trav_fileinfo_add(trav_info_t *info, hid_t loc_id)
     H5O_info_t oinfo;
     size_t     idx = info->nused - 1;
 
-    if (info->paths[idx].path && HDstrcmp(info->paths[idx].path, "."))
+    if (info->paths[idx].path && HDstrcmp(info->paths[idx].path, ".") != 0)
         H5Oget_info_by_name2(loc_id, info->paths[idx].path, &oinfo, H5O_INFO_BASIC, H5P_DEFAULT);
     else
         H5Oget_info2(loc_id, &oinfo, H5O_INFO_BASIC);
@@ -718,7 +718,7 @@ trav_table_addlink(trav_table_t *table, haddr_t objno, const char *path)
  *-------------------------------------------------------------------------
  */
 void
-trav_table_addflags(unsigned *flags, char *name, h5trav_type_t type, trav_table_t *table)
+trav_table_addflags(const unsigned *flags, char *name, h5trav_type_t type, trav_table_t *table)
 {
     size_t new_obj;
 
diff --git a/tools/lib/h5trav.h b/tools/lib/h5trav.h
index cda27a2..8708bc9 100644
--- a/tools/lib/h5trav.h
+++ b/tools/lib/h5trav.h
@@ -186,6 +186,7 @@ H5TOOLS_DLL void trav_table_init(trav_table_t **table);
 
 H5TOOLS_DLL void trav_table_free(trav_table_t *table);
 
-H5TOOLS_DLL void trav_table_addflags(unsigned *flags, char *objname, h5trav_type_t type, trav_table_t *table);
+H5TOOLS_DLL void trav_table_addflags(const unsigned *flags, char *objname, h5trav_type_t type,
+                                     trav_table_t *table);
 
 #endif /* H5TRAV_H */