Hdf5 merge pr 509 v112 (#539)

* 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.

* Removes c99_(v)snprintf() calls from the standalone test code (#509)

* Committing clang-format changes

* Removes c99_(v)snprintf from standalone code

These internal API calls were removed in a previous commit but were
missed in the sio/pio_standalone code.

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

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>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

tools/test/perform/pio_standalone.h

@@ -348,15 +348,9 @@ H5_DLL int HDrand(void);
 #define HDsin(X)               sin(X)
 #define HDsinh(X)              sinh(X)
 #define HDsleep(N)             sleep(N)
-#ifdef H5_HAVE_WIN32_API
-H5_DLL int c99_snprintf(char *str, size_t size, const char *format, ...);
-#define HDsnprintf c99_snprintf /*varargs*/
-#else
-#define HDsnprintf snprintf /*varargs*/
-#endif
-/* sprintf() variable arguments */
-#define HDsprintf sprintf /*varargs*/
-#define HDsqrt(X) sqrt(X)
+#define HDsnprintf             snprintf /*varargs*/
+#define HDsprintf              sprintf  /*varargs*/
+#define HDsqrt(X)              sqrt(X)
 #ifdef H5_HAVE_RAND_R
 H5_DLL void HDsrand(unsigned int seed);
 #define HDsrandom(S) HDsrand(S)
@@ -367,7 +361,6 @@ H5_DLL void HDsrand(unsigned int seed);
 #define HDsrand(S)   srand(S)
 #define HDsrandom(S) srand(S)
 #endif
-/* sscanf() variable arguments */
 
 #ifdef H5_HAVE_WIN32_API
 #define HDstrcasecmp(A, B) _stricmp(A, B)
@@ -429,25 +422,20 @@ H5_DLL int64_t HDstrtoll(const char *s, const char **rest, int base);
 #else
 #define HDunlink(S) unlink(S)
 #endif
-#define HDutime(S, T)            utime(S, T)
-#define HDva_arg(A, T)           va_arg(A, T)
-#define HDva_end(A)              va_end(A)
-#define HDva_start(A, P)         va_start(A, P)
-#define HDvasprintf(RET, FMT, A) vasprintf(RET, FMT, A)
-#define HDvfprintf(F, FMT, A)    vfprintf(F, FMT, A)
-#define HDvprintf(FMT, A)        vprintf(FMT, A)
-#define HDvsprintf(S, FMT, A)    vsprintf(S, FMT, A)
-#ifdef H5_HAVE_WIN32_API
-H5_DLL int c99_vsnprintf(char *str, size_t size, const char *format, va_list ap);
-#define HDvsnprintf c99_vsnprintf
-#else
+#define HDutime(S, T)             utime(S, T)
+#define HDva_arg(A, T)            va_arg(A, T)
+#define HDva_end(A)               va_end(A)
+#define HDva_start(A, P)          va_start(A, P)
+#define HDvasprintf(RET, FMT, A)  vasprintf(RET, FMT, A)
+#define HDvfprintf(F, FMT, A)     vfprintf(F, FMT, A)
+#define HDvprintf(FMT, A)         vprintf(FMT, A)
+#define HDvsprintf(S, FMT, A)     vsprintf(S, FMT, A)
 #define HDvsnprintf(S, N, FMT, A) vsnprintf(S, N, FMT, A)
-#endif
-#define HDwait(W)           wait(W)
-#define HDwaitpid(P, W, O)  waitpid(P, W, O)
-#define HDwcstombs(S, P, Z) wcstombs(S, P, Z)
-#define HDwctomb(S, C)      wctomb(S, C)
-#define HDwrite(F, M, Z)    write(F, M, Z)
+#define HDwait(W)                 wait(W)
+#define HDwaitpid(P, W, O)        waitpid(P, W, O)
+#define HDwcstombs(S, P, Z)       wcstombs(S, P, Z)
+#define HDwctomb(S, C)            wctomb(S, C)
+#define HDwrite(F, M, Z)          write(F, M, Z)
 
 /*
  * And now for a couple non-Posix functions...  Watch out for systems that

tools/test/perform/sio_standalone.h

@@ -363,15 +363,9 @@ H5_DLL int HDrand(void);
 #define HDsin(X)               sin(X)
 #define HDsinh(X)              sinh(X)
 #define HDsleep(N)             sleep(N)
-#ifdef H5_HAVE_WIN32_API
-H5_DLL int c99_snprintf(char *str, size_t size, const char *format, ...);
-#define HDsnprintf c99_snprintf /*varargs*/
-#else
-#define HDsnprintf snprintf /*varargs*/
-#endif
-/* sprintf() variable arguments */
-#define HDsprintf sprintf /*varargs*/
-#define HDsqrt(X) sqrt(X)
+#define HDsnprintf             snprintf /*varargs*/
+#define HDsprintf              sprintf  /*varargs*/
+#define HDsqrt(X)              sqrt(X)
 #ifdef H5_HAVE_RAND_R
 H5_DLL void HDsrand(unsigned int seed);
 #define HDsrandom(S) HDsrand(S)
@@ -382,7 +376,6 @@ H5_DLL void HDsrand(unsigned int seed);
 #define HDsrand(S)   srand(S)
 #define HDsrandom(S) srand(S)
 #endif
-/* sscanf() variable arguments */
 
 #ifdef H5_HAVE_WIN32_API
 #define HDstrcasecmp(A, B) _stricmp(A, B)
@@ -444,25 +437,20 @@ H5_DLL int64_t HDstrtoll(const char *s, const char **rest, int base);
 #else
 #define HDunlink(S) unlink(S)
 #endif
-#define HDutime(S, T)            utime(S, T)
-#define HDva_arg(A, T)           va_arg(A, T)
-#define HDva_end(A)              va_end(A)
-#define HDva_start(A, P)         va_start(A, P)
-#define HDvasprintf(RET, FMT, A) vasprintf(RET, FMT, A)
-#define HDvfprintf(F, FMT, A)    vfprintf(F, FMT, A)
-#define HDvprintf(FMT, A)        vprintf(FMT, A)
-#define HDvsprintf(S, FMT, A)    vsprintf(S, FMT, A)
-#ifdef H5_HAVE_WIN32_API
-H5_DLL int c99_vsnprintf(char *str, size_t size, const char *format, va_list ap);
-#define HDvsnprintf c99_vsnprintf
-#else
+#define HDutime(S, T)             utime(S, T)
+#define HDva_arg(A, T)            va_arg(A, T)
+#define HDva_end(A)               va_end(A)
+#define HDva_start(A, P)          va_start(A, P)
+#define HDvasprintf(RET, FMT, A)  vasprintf(RET, FMT, A)
+#define HDvfprintf(F, FMT, A)     vfprintf(F, FMT, A)
+#define HDvprintf(FMT, A)         vprintf(FMT, A)
+#define HDvsprintf(S, FMT, A)     vsprintf(S, FMT, A)
 #define HDvsnprintf(S, N, FMT, A) vsnprintf(S, N, FMT, A)
-#endif
-#define HDwait(W)           wait(W)
-#define HDwaitpid(P, W, O)  waitpid(P, W, O)
-#define HDwcstombs(S, P, Z) wcstombs(S, P, Z)
-#define HDwctomb(S, C)      wctomb(S, C)
-#define HDwrite(F, M, Z)    write(F, M, Z)
+#define HDwait(W)                 wait(W)
+#define HDwaitpid(P, W, O)        waitpid(P, W, O)
+#define HDwcstombs(S, P, Z)       wcstombs(S, P, Z)
+#define HDwctomb(S, C)            wctomb(S, C)
+#define HDwrite(F, M, Z)          write(F, M, Z)
 
 /*
  * And now for a couple non-Posix functions...  Watch out for systems that