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>

4 files changed, 45 insertions, 45 deletions

diff --git a/tools/test/h5diff/h5diffgentest.c b/tools/test/h5diff/h5diffgentest.c
index cf60a6a..f03254e 100644
--- a/tools/test/h5diff/h5diffgentest.c
+++ b/tools/test/h5diff/h5diffgentest.c
@@ -465,15 +465,15 @@ test_basic(const char *fname1, const char *fname2, const char *fname3)
         float data15[6];
         float data16[6];
 
-        data15[0] = (float)HDsqrt(-1.0F);
+        data15[0] = (float)HDsqrt(-1.0);
         data15[1] = 1.0F;
-        data15[2] = (float)HDsqrt(-1.0F);
+        data15[2] = (float)HDsqrt(-1.0);
         data15[3] = 1.0F;
         data15[4] = 1.0F;
         data15[5] = 1.0F;
 
-        data16[0] = (float)HDsqrt(-1.0F);
-        data16[1] = (float)HDsqrt(-1.0F);
+        data16[0] = (float)HDsqrt(-1.0);
+        data16[1] = (float)HDsqrt(-1.0);
         data16[2] = 1.0F;
         data16[3] = 1.0F;
         data16[4] = 1.0F;
@@ -492,19 +492,19 @@ test_basic(const char *fname1, const char *fname2, const char *fname3)
         double data17[6];
         double data18[6];
 
-        data17[0] = HDsqrt(-1.0F);
-        data17[1] = 1.0F;
-        data17[2] = HDsqrt(-1.0F);
-        data17[3] = 1.0F;
-        data17[4] = 1.0F;
-        data17[5] = 1.0F;
+        data17[0] = HDsqrt(-1.0);
+        data17[1] = 1.0;
+        data17[2] = HDsqrt(-1.0);
+        data17[3] = 1.0;
+        data17[4] = 1.0;
+        data17[5] = 1.0;
 
-        data18[0] = HDsqrt(-1.0F);
-        data18[1] = HDsqrt(-10000.0F);
-        data18[2] = 1.0F;
-        data18[3] = 1.0F;
-        data18[4] = 1.0F;
-        data18[5] = 1.0F;
+        data18[0] = HDsqrt(-1.0);
+        data18[1] = HDsqrt(-10000.0);
+        data18[2] = 1.0;
+        data18[3] = 1.0;
+        data18[4] = 1.0;
+        data18[5] = 1.0;
 
         write_dset(gid1, 1, dims1, "fp17", H5T_NATIVE_DOUBLE, data17);
         write_dset(gid1, 1, dims1, "fp18", H5T_NATIVE_DOUBLE, data18);
@@ -519,11 +519,11 @@ test_basic(const char *fname1, const char *fname2, const char *fname3)
         float  data19[6];
         double data20[6];
 
-        data19[0] = data19[1] = data19[2] = (float)HDlog(0.0F);
-        data19[3] = data19[4] = data19[5] = (float)-HDlog(0.0F);
+        data19[0] = data19[1] = data19[2] = (float)HDlog(0.0);
+        data19[3] = data19[4] = data19[5] = (float)-HDlog(0.0);
 
-        data20[0] = data20[1] = data20[2] = HDlog(0.0F);
-        data20[3] = data20[4] = data20[5] = -HDlog(0.0F);
+        data20[0] = data20[1] = data20[2] = HDlog(0.0);
+        data20[3] = data20[4] = data20[5] = -HDlog(0.0);
 
         write_dset(gid1, 1, dims1, "fp19", H5T_NATIVE_FLOAT, data19);
         write_dset(gid1, 1, dims1, "fp19_COPY", H5T_NATIVE_FLOAT, data19);
@@ -547,13 +547,13 @@ test_basic(const char *fname1, const char *fname2, const char *fname3)
         size_t  type_size;
         hid_t   tid;
 
-        buf1[0].d = HDsqrt(-1.0F);
-        buf1[0].f = (float)HDsqrt(-1.0F);
-        buf2[0].d = HDsqrt(-1.0F);
-        buf2[0].f = (float)HDsqrt(-1.0F);
+        buf1[0].d = HDsqrt(-1.0);
+        buf1[0].f = (float)HDsqrt(-1.0);
+        buf2[0].d = HDsqrt(-1.0);
+        buf2[0].f = (float)HDsqrt(-1.0);
 
-        buf1[1].d = HDsqrt(-1.0F);
-        buf1[1].f = (float)HDsqrt(-1.0F);
+        buf1[1].d = HDsqrt(-1.0);
+        buf1[1].f = (float)HDsqrt(-1.0);
         buf2[1].d = 0.0F;
         buf2[1].f = 0.0F;
 
diff --git a/tools/test/h5repack/h5repackgentest.c b/tools/test/h5repack/h5repackgentest.c
index 2b94422..576b1c7 100644
--- a/tools/test/h5repack/h5repackgentest.c
+++ b/tools/test/h5repack/h5repackgentest.c
@@ -72,8 +72,8 @@ struct external_def {
  * Returns 0 on success, -1 on failure.
  */
 static int
-__make_dataset(hid_t file_id, const char *dset_name, hid_t mem_type_id, hid_t space_id, hid_t dcpl_id,
-               void *wdata)
+make_dataset(hid_t file_id, const char *dset_name, hid_t mem_type_id, hid_t space_id, hid_t dcpl_id,
+             void *wdata)
 {
     hid_t dset_id   = H5I_INVALID_HID;
     int   ret_value = 0;
@@ -90,7 +90,7 @@ done:
         (void)H5Dclose(dset_id);
 
     return ret_value;
-} /* end __make_dataset() */
+} /* end make_dataset() */
 
 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  * Helper function to populate the DCPL external storage list.
@@ -101,8 +101,8 @@ done:
  * Returns 0 on success, -1 on failure.
  */
 static int
-__set_dcpl_external_list(hid_t dcpl, const char *filename, unsigned n_elts_per_file, unsigned n_elts_total,
-                         hsize_t elt_size)
+set_dcpl_external_list(hid_t dcpl, const char *filename, unsigned n_elts_per_file, unsigned n_elts_total,
+                       hsize_t elt_size)
 {
     char     name[MAX_NAME_SIZE];
     unsigned n_external_files = 0;
@@ -123,7 +123,7 @@ __set_dcpl_external_list(hid_t dcpl, const char *filename, unsigned n_elts_per_f
             return -1;
     }
     return 0;
-} /* end __set_dcpl_external_list() */
+} /* end set_dcpl_external_list() */
 
 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  * Generalized utility function to write a file with the specified data and
@@ -132,8 +132,8 @@ __set_dcpl_external_list(hid_t dcpl, const char *filename, unsigned n_elts_per_f
  * Returns 0 on success, -1 on failure.
  */
 static int
-__make_file(const char *basename, struct external_def *ext, hid_t type_id, hsize_t rank, hsize_t *dims,
-            void *wdata)
+make_file(const char *basename, struct external_def *ext, hid_t type_id, hsize_t rank, hsize_t *dims,
+          void *wdata)
 {
     char  filename[MAX_NAME_SIZE];
     hid_t file_id   = H5I_INVALID_HID;
@@ -149,8 +149,8 @@ __make_file(const char *basename, struct external_def *ext, hid_t type_id, hsize
         if (dcpl_id == H5I_INVALID_HID)
             H5REPACKGENTEST_OOPS;
 
-        if (__set_dcpl_external_list(dcpl_id, basename, ext->n_elts_per_file, ext->n_elts_total,
-                                     ext->type_size) < 0)
+        if (set_dcpl_external_list(dcpl_id, basename, ext->n_elts_per_file, ext->n_elts_total,
+                                   ext->type_size) < 0)
             H5REPACKGENTEST_OOPS;
     }
 
@@ -162,13 +162,13 @@ __make_file(const char *basename, struct external_def *ext, hid_t type_id, hsize
     if (file_id == H5I_INVALID_HID)
         H5REPACKGENTEST_OOPS;
 
-    if (__make_dataset(file_id, "dset", type_id, space_id, dcpl_id, wdata) < 0)
+    if (make_dataset(file_id, "dset", type_id, space_id, dcpl_id, wdata) < 0)
         H5REPACKGENTEST_OOPS;
 
 done:
     H5REPACKGENTEST_COMMON_CLEANUP(dcpl_id, file_id, space_id);
     return ret_value;
-} /* end __make_file() */
+} /* end make_file() */
 
 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  * Returns 0 on success, -1 on failure.
@@ -190,7 +190,7 @@ generate_int32le_1d(hbool_t external)
     }
 
     def_ptr = (TRUE == external) ? (&def) : NULL;
-    if (__make_file(FILE_INT32LE_1, def_ptr, H5T_STD_I32LE, 1, dims, wdata) < 0)
+    if (make_file(FILE_INT32LE_1, def_ptr, H5T_STD_I32LE, 1, dims, wdata) < 0)
         ret_value = -1;
 
     return ret_value;
@@ -216,7 +216,7 @@ generate_int32le_2d(hbool_t external)
     }
 
     def_ptr = (TRUE == external) ? (&def) : NULL;
-    if (__make_file(FILE_INT32LE_2, def_ptr, H5T_STD_I32LE, 2, dims, wdata) < 0)
+    if (make_file(FILE_INT32LE_2, def_ptr, H5T_STD_I32LE, 2, dims, wdata) < 0)
         ret_value = -1;
 
     return ret_value;
@@ -249,7 +249,7 @@ generate_int32le_3d(hbool_t external)
     }
 
     def_ptr = (TRUE == external) ? (&def) : NULL;
-    if (__make_file(FILE_INT32LE_3, def_ptr, H5T_STD_I32LE, 3, dims, wdata) < 0)
+    if (make_file(FILE_INT32LE_3, def_ptr, H5T_STD_I32LE, 3, dims, wdata) < 0)
         ret_value = -1;
 
     return ret_value;
@@ -282,7 +282,7 @@ generate_uint8be(hbool_t external)
     }
 
     def_ptr = (TRUE == external) ? (&def) : NULL;
-    if (__make_file(FILE_UINT8BE, def_ptr, H5T_STD_U8BE, 3, dims, wdata) < 0)
+    if (make_file(FILE_UINT8BE, def_ptr, H5T_STD_U8BE, 3, dims, wdata) < 0)
         ret_value = -1;
 
     return ret_value;
@@ -312,7 +312,7 @@ generate_f32le(hbool_t external)
     }
 
     def_ptr = (TRUE == external) ? (&def) : NULL;
-    if (__make_file(FILE_F32LE, def_ptr, H5T_IEEE_F32LE, 2, dims, wdata) < 0)
+    if (make_file(FILE_F32LE, def_ptr, H5T_IEEE_F32LE, 2, dims, wdata) < 0)
         ret_value = -1;
 
     return ret_value;
diff --git a/tools/test/perform/sio_engine.c b/tools/test/perform/sio_engine.c
index f8061d4..e5a0ec8 100644
--- a/tools/test/perform/sio_engine.c
+++ b/tools/test/perform/sio_engine.c
@@ -80,7 +80,7 @@ static int clean_file_g = -1; /*whether to cleanup temporary test     */
 /*0 is no cleanup; 1 is do cleanup      */
 
 /* the different types of file descriptors we can expect */
-typedef union _file_descr {
+typedef union {
     int   posixfd; /* POSIX file handle*/
     hid_t h5fd;    /* HDF5 file        */
 } file_descr;
diff --git a/tools/test/perform/sio_perf.c b/tools/test/perform/sio_perf.c
index 8463ffa..5b3a9e8 100644
--- a/tools/test/perform/sio_perf.c
+++ b/tools/test/perform/sio_perf.c
@@ -292,7 +292,7 @@ struct options {
     size_t      page_size;
 };
 
-typedef struct _minmax {
+typedef struct {
     double min;
     double max;
     double sum;