Hdf5 merge issue #458 to hdf5_1_12 (#463)

* Snapshot version 1.12 release 1-3.  Update  version to 1.12.1-4.

* First cut of the H5 public API documentation. (#80)

* First cut of the H5 public API documentation.

* Added H5Z "bonus track."

* Applied Quincey's patch.

* Added the missing patches from Quincey's original patch.

* H5PL (complete) and basic H5VL API documentation.

* Added H5I API docs.

* Added H5L API docs.

* First installment from Elena's H5T batch.

* Second installment of Elena's H5T batch.

* Final installment of Elena's H5T batch.

* Full set of current H5F documentation. (#105)

* First cut of the H5 public API documentation.

* Added H5Z "bonus track."

* Applied Quincey's patch.

* Added the missing patches from Quincey's original patch.

* H5PL (complete) and basic H5VL API documentation.

* Added H5I API docs.

* Added H5L API docs.

* First installment from Elena's H5T batch.

* Second installment of Elena's H5T batch.

* Final installment of Elena's H5T batch.

* Migrated documentation for SWMR functions.

* Catching up on MDC functions.

* Integrated the H5F MDC function documentation.

* Added MDC and parallel H5F functions.

* Slightly updated main page.

* Added doxygen/dox/H5AC_cache_config_t.dox to MANIFEST.

* Doxygen - added (mostly) beginner functions (#112)

* Doxygen - added (mostly) beginner functions

* Removed duplicate H5Pset_szip function

* Add src/H5module.h to MANIFEST.

* close #195. (#196)

* Update HDF5PluginMacros.cmake

* Update HDF5PluginMacros.cmake

* Avoid aligned access for references by decoding into temporary buffer and then copying the result into the actual buffer.   Update test to be more thorough with using compound datatype fields everywhere. (#206)

* 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.

* Fixes various warnings noticed on Windows (#425)

* Fixes various warnings noticed on Windows

- Adds a prototype for our implementation of vasprintf
- Return type of H5_get_utf16_str() is now non-const
- Fixes possible uninitialized return type in Wremove_utf8
- Better isolation of fork() code in accum.c:test_swmr_write_big()
- Better isolation of non-zlib code in dsets.c:test_filter_delete()
- Removed unused variable in trefer.c:test_reference_cmpnd_obj()

* Fixes clang-format issues

* 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>

* Remove 2 functions incorrectly merged from develop in a cherry-pick merge of PR #451.

Co-authored-by: Gerd Heber <gheber@hdfgroup.org>
Co-authored-by: bljhdf <58825073+bljhdf@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Quincey Koziol <quincey@koziol.cc>
Co-authored-by: Sean McBride <sean@rogue-research.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>

8 files changed, 32 insertions, 29 deletions

diff --git a/hl/c++/test/ptableTest.cpp b/hl/c++/test/ptableTest.cpp
index bf60402..8e71557 100644
--- a/hl/c++/test/ptableTest.cpp
+++ b/hl/c++/test/ptableTest.cpp
@@ -690,7 +690,7 @@ TestHDFFV_9758()
 
             if (s2.a != s1[i].a || s2.e != s1[i].e)
                 goto error;
-            else if (HDstrcmp(s2.d, s1[i].d))
+            else if (HDstrcmp(s2.d, s1[i].d) != 0)
                 goto error;
         }
     } // end of ptable block
diff --git a/hl/test/test_file_image.c b/hl/test/test_file_image.c
index c20112f..f820568 100644
--- a/hl/test/test_file_image.c
+++ b/hl/test/test_file_image.c
@@ -51,7 +51,7 @@
  *-------------------------------------------------------------------------
  */
 static int
-test_file_image(size_t open_images, size_t nflags, unsigned *flags)
+test_file_image(size_t open_images, size_t nflags, const unsigned *flags)
 {
     hid_t * file_id, *dset_id, file_space, plist; /* HDF5 ids */
     hsize_t dims1[RANK]    = {2, 3};              /* original dimension of datasets */
diff --git a/hl/test/test_ld.c b/hl/test/test_ld.c
index 06cb600..02a56f4 100644
--- a/hl/test/test_ld.c
+++ b/hl/test/test_ld.c
@@ -157,7 +157,8 @@ static herr_t test_LD_elmts_invalid(const char *file);
 static herr_t test_LD_elmts_one(const char *file, const char *dname, const char *fields);
 static herr_t test_LD_elmts_two(const char *file, const char *dname, const char *fields);
 
-static herr_t verify_elmts_two(int type, hsize_t *ext_dims, hsize_t *prev_dims, void *_ldbuf, void *_buf);
+static herr_t verify_elmts_two(int type, const hsize_t *ext_dims, const hsize_t *prev_dims, void *_ldbuf,
+                               void *_buf);
 
 /* data structures for compound data type */
 typedef struct sub22_t {
@@ -1135,7 +1136,7 @@ error:
  **************************************************************************************
  */
 static herr_t
-verify_elmts_two(int type, hsize_t *ext_dims, hsize_t *prev_dims, void *_ldbuf, void *_buf)
+verify_elmts_two(int type, const hsize_t *ext_dims, const hsize_t *prev_dims, void *_ldbuf, void *_buf)
 {
     int k, m; /* Local index variable */
 
diff --git a/hl/test/test_lite.c b/hl/test/test_lite.c
index 52cda54..cae91ff 100644
--- a/hl/test/test_lite.c
+++ b/hl/test/test_lite.c
@@ -1054,7 +1054,7 @@ test_integers(void)
         HDfree(dt_str);
         goto out;
     }
-    if (HDstrcmp(dt_str, "H5T_STD_I8BE")) {
+    if (HDstrcmp(dt_str, "H5T_STD_I8BE") != 0) {
         HDfree(dt_str);
         goto out;
     }
@@ -1112,7 +1112,7 @@ test_fps(void)
         HDfree(dt_str);
         goto out;
     }
-    if (HDstrcmp(dt_str, "H5T_IEEE_F32BE")) {
+    if (HDstrcmp(dt_str, "H5T_IEEE_F32BE") != 0) {
         HDfree(dt_str);
         goto out;
     }
@@ -1184,7 +1184,7 @@ test_strings(void)
         goto out;
     }
     if (HDstrcmp(dt_str, "H5T_STRING {\n      STRSIZE 13;\n      STRPAD H5T_STR_NULLTERM;\n      CSET "
-                         "H5T_CSET_ASCII;\n      CTYPE H5T_C_S1;\n   }")) {
+                         "H5T_CSET_ASCII;\n      CTYPE H5T_C_S1;\n   }") != 0) {
         HDprintf("dt=\n%s\n", dt_str);
         HDfree(dt_str);
         goto out;
@@ -1219,7 +1219,7 @@ test_strings(void)
         goto out;
     }
     if (HDstrcmp(dt_str, "H5T_STRING {\n      STRSIZE H5T_VARIABLE;\n      STRPAD H5T_STR_NULLPAD;\n      "
-                         "CSET H5T_CSET_ASCII;\n      CTYPE H5T_C_S1;\n   }")) {
+                         "CSET H5T_CSET_ASCII;\n      CTYPE H5T_C_S1;\n   }") != 0) {
         HDprintf("dt=\n%s\n", dt_str);
         HDfree(dt_str);
         goto out;
@@ -1238,7 +1238,7 @@ test_strings(void)
     if (HDstrncmp(dt_str,
                   "H5T_STRING {\n      STRSIZE H5T_VARIABLE;\n      STRPAD H5T_STR_NULLPAD;\n      CSET "
                   "H5T_CSET_ASCII;\n      CTYPE H5T_C_S1;\n   }",
-                  str_len - 1)) {
+                  str_len - 1) != 0) {
         HDprintf("dt=\n%s\n", dt_str);
         HDfree(dt_str);
         goto out;
@@ -1261,7 +1261,7 @@ test_strings(void)
     if (HDstrncmp(dt_str,
                   "H5T_STRING {\n      STRSIZE H5T_VARIABLE;\n      STRPAD H5T_STR_NULLPAD;\n      CSET "
                   "H5T_CSET_ASCII;\n      CTYPE H5T_C_S1;\n   }",
-                  str_len)) {
+                  str_len) != 0) {
         HDprintf("dt=\n%s\n", dt_str);
         HDfree(dt_str);
         goto out;
@@ -1322,7 +1322,8 @@ test_opaques(void)
     }
     if (HDstrcmp(
             dt_str,
-            "H5T_OPAQUE {\n      OPQ_SIZE 19;\n      OPQ_TAG \"This is a tag for opaque type\";\n   }")) {
+            "H5T_OPAQUE {\n      OPQ_SIZE 19;\n      OPQ_TAG \"This is a tag for opaque type\";\n   }") !=
+        0) {
         HDprintf("dt=\n%s\n", dt_str);
         HDfree(dt_str);
         goto out;
@@ -1376,7 +1377,7 @@ test_enums(void)
 
     if (H5Tenum_nameof(dtype, &value1, name1, size) < 0)
         goto out;
-    if (HDstrcmp(name1, "BLUE"))
+    if (HDstrcmp(name1, "BLUE") != 0)
         goto out;
 
     if (H5Tenum_valueof(dtype, name2, &value2) < 0)
@@ -1399,8 +1400,9 @@ test_enums(void)
         HDfree(dt_str);
         goto out;
     }
-    if (HDstrcmp(dt_str, "H5T_ENUM {\n      H5T_STD_I32LE;\n      \"RED\"              5;\n      \"GREEN\"   "
-                         "         6;\n      \"BLUE\"             7;\n      \"WHITE\"            8;\n   }")) {
+    if (HDstrcmp(dt_str,
+                 "H5T_ENUM {\n      H5T_STD_I32LE;\n      \"RED\"              5;\n      \"GREEN\"   "
+                 "         6;\n      \"BLUE\"             7;\n      \"WHITE\"            8;\n   }") != 0) {
 
         HDprintf("dt=\n%s\n", dt_str);
         HDfree(dt_str);
@@ -1462,7 +1464,7 @@ test_variables(void)
         HDfree(dt_str);
         goto out;
     }
-    if (HDstrcmp(dt_str, "H5T_VLEN {\n      H5T_VLEN {\n         H5T_STD_I32BE\n      }\n   }")) {
+    if (HDstrcmp(dt_str, "H5T_VLEN {\n      H5T_VLEN {\n         H5T_STD_I32BE\n      }\n   }") != 0) {
         HDprintf("dt=\n%s\n", dt_str);
         HDfree(dt_str);
         goto out;
@@ -1526,7 +1528,7 @@ test_arrays(void)
     }
     if (HDstrcmp(dt_str, "H5T_ARRAY {\n      [5][7][13] H5T_ARRAY {\n         [17][19] H5T_COMPOUND {\n      "
                          "      H5T_STD_I8BE \"arr_compound_1\" : 0;\n            H5T_STD_I32BE "
-                         "\"arr_compound_2\" : 1;\n         }\n      }\n   }")) {
+                         "\"arr_compound_2\" : 1;\n         }\n      }\n   }") != 0) {
         HDprintf("dt=\n%s\n", dt_str);
         HDfree(dt_str);
         goto out;
@@ -1586,7 +1588,7 @@ test_compounds(void)
         goto out;
     }
     if (HDstrcmp(dt_str, "H5T_COMPOUND {\n      H5T_STD_I16BE \"one_field\" : 2;\n      H5T_STD_U8LE "
-                         "\"two_field\" : 6;\n   }")) {
+                         "\"two_field\" : 6;\n   }") != 0) {
         HDprintf("dt=\n%s\n", dt_str);
         HDfree(dt_str);
         goto out;
@@ -1605,7 +1607,7 @@ test_compounds(void)
 
     if ((memb_name = H5Tget_member_name(dtype, 1)) == NULL)
         goto out;
-    if (HDstrcmp(memb_name, "i16_field")) {
+    if (HDstrcmp(memb_name, "i16_field") != 0) {
         H5free_memory(memb_name);
         goto out;
     }
@@ -1683,7 +1685,7 @@ test_compound_bug(void)
 
     if ((memb_name = H5Tget_member_name(dtype, 2)) == NULL)
         goto out;
-    if (HDstrcmp(memb_name, "sub")) {
+    if (HDstrcmp(memb_name, "sub") != 0) {
         H5free_memory(memb_name);
         goto out;
     }
@@ -1720,7 +1722,7 @@ test_compound_bug(void)
     if ((memb_name = H5Tget_member_name(dtype, 1)) == NULL)
         goto out;
     if (HDstrcmp(memb_name, "desc____________________________________________________________________________"
-                            "_____________")) {
+                            "_____________") != 0) {
         H5free_memory(memb_name);
         goto out;
     }
diff --git a/hl/tools/gif2h5/gif.h b/hl/tools/gif2h5/gif.h
index 2b4a344..1a8cfe4 100644
--- a/hl/tools/gif2h5/gif.h
+++ b/hl/tools/gif2h5/gif.h
@@ -157,8 +157,8 @@ int ReadGifApplication(GIFAPPLICATION *, GIFBYTE **);
 int ReadGifComment(GIFCOMMENT *, GIFBYTE **);
 
 /* HDFGIFWR.C */
-int hdfWriteGIF(FILE *fp, GIFBYTE *pic, int ptype, int w, int h, GIFBYTE *rmap, GIFBYTE *gmap, GIFBYTE *bmap,
-                GIFBYTE *pc2ncmap, int numcols, int colorstyle, int BitsPerPixel);
+int hdfWriteGIF(FILE *fp, GIFBYTE *pic, int ptype, int w, int h, const GIFBYTE *rmap, const GIFBYTE *gmap,
+                const GIFBYTE *bmap, const GIFBYTE *pc2ncmap, int numcols, int colorstyle, int BitsPerPixel);
 
 /* WRITEHDF.C */
 int WriteHDF(GIFTOMEM, GIFCHAR *);
@@ -176,7 +176,7 @@ int ReadHDF(GIFBYTE **data, GIFBYTE palette[256][3], hsize_t *image_size, GIFCHA
             GIFCHAR *dset_name, GIFCHAR *pal_name);
 
 GIFBYTE *Decompress(GIFIMAGEDESC *, GIFHEAD *);
-GIFBYTE  GetByte(GIFBYTE *);
+GIFBYTE  GetByte(const GIFBYTE *);
 GIFWORD  GetWord(GIFBYTE *);
 
 void cleanup(GIFBYTE *);
diff --git a/hl/tools/gif2h5/gifread.c b/hl/tools/gif2h5/gifread.c
index b88264b..d2afbc4 100644
--- a/hl/tools/gif2h5/gifread.c
+++ b/hl/tools/gif2h5/gifread.c
@@ -38,7 +38,7 @@ GetWord(GIFBYTE *MemGif)
 }
 
 GIFBYTE
-GetByte(GIFBYTE *MemGif) { return *MemGif; }
+GetByte(const GIFBYTE *MemGif) { return *MemGif; }
 
 /*
  *  Read a GIF image GIFBYTE Header.
@@ -62,7 +62,7 @@ ReadGifHeader(GIFHEAD * GifHead, /* Pointer to GIF header structure  */
         GifHead->HeaderDump[i] = *(*MemGif2)++;
     }
 
-    if (strncmp((const char *)GifHead->HeaderDump, "GIF", (size_t)3)) {
+    if (strncmp((const char *)GifHead->HeaderDump, "GIF", (size_t)3) != 0) {
         printf("The file does not appear to be a valid GIF file.\n");
         exit(EXIT_FAILURE);
     }
diff --git a/hl/tools/gif2h5/hdfgifwr.c b/hl/tools/gif2h5/hdfgifwr.c
index 8068829..21b14d1 100644
--- a/hl/tools/gif2h5/hdfgifwr.c
+++ b/hl/tools/gif2h5/hdfgifwr.c
@@ -135,8 +135,8 @@ static int EOFCode;
 
 /*************************************************************/
 int
-hdfWriteGIF(FILE *fp, byte *pic, int ptype, int w, int h, byte *rmap, byte *gmap, byte *bmap, byte *pc2ncmap,
-            int numcols, int colorstyle, int BitsPerPixel)
+hdfWriteGIF(FILE *fp, byte *pic, int ptype, int w, int h, const byte *rmap, const byte *gmap,
+            const byte *bmap, const byte *pc2ncmap, int numcols, int colorstyle, int BitsPerPixel)
 {
     int   InitCodeSize;
     int   i;
diff --git a/hl/tools/h5watch/h5watch.c b/hl/tools/h5watch/h5watch.c
index 8d7f4ec..a5e82ca 100644
--- a/hl/tools/h5watch/h5watch.c
+++ b/hl/tools/h5watch/h5watch.c
@@ -43,7 +43,7 @@ static unsigned g_retry = DEFAULT_RETRY;  /* # of times to try opening the file
 static hbool_t  g_display_hex    = FALSE; /* display data in hexadecimal format : LATER */
 static hbool_t  g_user_interrupt = FALSE; /* Flag to indicate that user interrupted execution */
 
-static herr_t doprint(hid_t did, hsize_t *start, hsize_t *block, int rank);
+static herr_t doprint(hid_t did, const hsize_t *start, const hsize_t *block, int rank);
 static herr_t slicendump(hid_t did, hsize_t *prev_dims, hsize_t *cur_dims, hsize_t *start, hsize_t *block,
                          int rank, int subrank);
 static herr_t monitor_dataset(hid_t fid, char *dsetname);
@@ -95,7 +95,7 @@ static struct long_options l_opts[] = {{"help", no_arg, 'h'},         {"hel", no
  *-------------------------------------------------------------------------
  */
 static herr_t
-doprint(hid_t did, hsize_t *start, hsize_t *block, int rank)
+doprint(hid_t did, const hsize_t *start, const hsize_t *block, int rank)
 {
     h5tools_context_t ctx;                           /* print context  */
     h5tool_format_t   info;                          /* Format info for the tools library */