Hdf5 merge issue 537 v110 (#545)

* 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.

* Cleans up a couple of MSVC warnings in testhdf5 (#475)
* Fixes a few testhdf5 warnings raised in Visual Studio

Visual Studio is grumpier about treating pointers like integers than
gcc.

* Committing clang-format changes

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

* Fix typos and grammar errors. (#476)

* Suppresses the tcheck_version test's abort dialog on Windows (#477)

* Suppresses the tcheck_version test's abort dialog on Windows

Windows raises a modal abort/retry/ignore dialog box when CRT
calls abort(). This change installs a report hook that suppresses
the dialog so that the CMake tests don't time out waiting for a
nonexistent user to click a dialog box.

* Committing clang-format changes

* Removes __cdecl from callback

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

* More warning fixes (#400)

* Fixed -Wunused-local-typedef warning

* Fixed -Wformat warnings

In one case also removed a `z` character. There was a `z%d` that I think was supposed to be `%zd`

* Fixed -Wshorten-64-to-32 warnings

* Fixed -Wself-assign warnings

* Fixed -Wreserved-id-macro warnings

* Commit format changes from clang-format, clang version 10.0.1.

* Fixed -Wself-assign warnings

* Fixed -Wunused-local-typedef warning

* Fixed -Wformat warnings

In two cases also removed a `z` character. There was a `z%d` that was supposed to be `%zd`.

* Fixed -Wshorten-64-to-32 warnings

* Fixed -Wreserved-id-macro warnings

* Fixed -Wself-assign warnings

* Format source.

* Remove blank lines to pass format check.

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

* Changes found during merge to 1.12 (#414)

* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* OESS-98 fix tools test for plugins

* Keep doxygen comments under 100 chars long - format hint

* Whitespace

* HDFFV-11144 - Reclassify CMake messages

* HDFFV-11099/11100 added help text

* Reworked switch statement to compare string instead

* Fix typo

* Update CDash mode

* Correct name of threadsafe

* Correct option name

* Undo accidental commit

* Note LLVM 10 to 11 format default changes

* Update format plugin

* Undo clang-format version 11 changes

* One more correction

* Update supported platforms

* Revert whitespace changes

* Correct whitespace

* Changes from PR#3

* HDFFV-11213 added option to control gcc10 warnings diagnostics

* HDFFV-11212 Use the new references correctly in JNI utility and tests

* format source

* Fix typo

* Add new test file

* HDFFV-11212 - update test and remove unused arg

* Minor non-space formatting changes

* Use H5I_INVALID_ID instead of "-1"

* source formatting

* add missing testfile, update jni function

* Undo commit of debug code

* remove mislocated file

* Fix h5repack test for handling of fapls and id close

* Update h5diff test files usage text

* HDFFV-11212 add new ref tests for JNI export dataset

* src format update

* Remove blank line typo

* src format typo

* long double requires %Lg

* Another long double foramt specifer S.B. %Lg

* issue with t128bit test

* Windows issue with h5dump and type.

* Fix review issues

* refactor function nesting and fix error checks

* format fixes

* Remove untested functions and javadoc quiet comments

* Restore TRY block.

* Change string append errors to memory exception

* revert to H5_JNI_FATAL_ERROR - support functions need work

* Add assertion error for h5util functions

* remove duplicate function

* format fix

* Revert HD function error handling

* Update copyright comments

* GH #386 java folder copyright corrections

* Whitespace

* GH #359 implement and fix tools 1.6 API usage

* remove excessive comments

* Flip inits to correct ifdef section

* rework ifdef to be simpler

* format issue

* Reformat ifdef inits

* remove static attribute

* format compliance

* Update names

* Revert because logic relies on float not being int

* Changes noticed from creating merge of #412

* Double underscore change

* Correct compiler version variable used

* Remove header guard underscores

* Whitespace cleanup

* File locks now work on Windows (#480)

* File locks now work on Windows

Uses LockFileEx() and UnlockFileEx(). Fixes HDFFV-10191 (partial).

* Committing clang-format changes

* Committing clang-format changes

* Fixes commenting in h5repack

* Reworks H5Fis_accessible()

H5Fis_accessible() created a new file handle and attempted to read
through it, which will fail when a file has been opened with an
exclusive lock on operating systems that have mandatory locks.

This change uses the same scheme we use in H5Fopen() to check if
the file is already open and only tries to read the file signature
if the file has not already been opened.

Also adds a test for this behavior.

* Committing clang-format changes

* Trivial change to force github to run actions

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

* small edits (#481)

* fixed missed closing of a dataset

* fixed missed closing of a dataset

* fixed typo in error return

* Committing clang-format changes

* minor edits

* code format

* Committing clang-format changes

* code format

* minor edit

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

* Adds an implementation for nanosleep on Windows (#483)

* Adds an implementation for nanosleep on Windows

* Committing clang-format changes

* Fix insane formatter issue

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

* Updates HSYS_GOTO_ERROR to emit GetLastError() values on Win32 (#492)

* Committing clang-format changes

* Updates H5SYS_GOTO_ERROR to emit Win32's GetLastError()

* Committing clang-format changes

* Format source changes

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

* Updates that allow accum SWMR tests to work on Windows (#493)

* Committing clang-format changes

* Updates the accum test to work on Windows

Uses CreateProcess() on Windows

* Source formatting

* Fix for Unix child result

* Fixes process return code bug on Windows

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

* Disable long double tests and remove CMake flag groups (#494)

* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* OESS-98 fix tools test for plugins

* Keep doxygen comments under 100 chars long - format hint

* Whitespace

* HDFFV-11144 - Reclassify CMake messages

* HDFFV-11099/11100 added help text

* Reworked switch statement to compare string instead

* Fix typo

* Update CDash mode

* Correct name of threadsafe

* Correct option name

* Undo accidental commit

* Note LLVM 10 to 11 format default changes

* Update format plugin

* Undo clang-format version 11 changes

* One more correction

* Update supported platforms

* Revert whitespace changes

* Correct whitespace

* Changes from PR#3

* HDFFV-11213 added option to control gcc10 warnings diagnostics

* HDFFV-11212 Use the new references correctly in JNI utility and tests

* format source

* Fix typo

* Add new test file

* HDFFV-11212 - update test and remove unused arg

* Minor non-space formatting changes

* Use H5I_INVALID_ID instead of "-1"

* source formatting

* add missing testfile, update jni function

* Undo commit of debug code

* remove mislocated file

* Fix h5repack test for handling of fapls and id close

* Update h5diff test files usage text

* HDFFV-11212 add new ref tests for JNI export dataset

* src format update

* Remove blank line typo

* src format typo

* long double requires %Lg

* Another long double foramt specifer S.B. %Lg

* issue with t128bit test

* Windows issue with h5dump and type.

* Fix review issues

* refactor function nesting and fix error checks

* format fixes

* Remove untested functions and javadoc quiet comments

* Restore TRY block.

* Change string append errors to memory exception

* revert to H5_JNI_FATAL_ERROR - support functions need work

* Add assertion error for h5util functions

* remove duplicate function

* format fix

* Revert HD function error handling

* Update copyright comments

* GH #386 java folder copyright corrections

* Whitespace

* GH #359 implement and fix tools 1.6 API usage

* remove excessive comments

* Flip inits to correct ifdef section

* rework ifdef to be simpler

* format issue

* Reformat ifdef inits

* remove static attribute

* format compliance

* Update names

* Revert because logic relies on float not being int

* Changes noticed from creating merge of #412

* Double underscore change

* Correct compiler version variable used

* Remove header guard underscores

* Whitespace cleanup

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* correct window os name

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* HDFFV-11113 long double in tools

* HDFFV-11113 add note

* Disable long double tests for now

* HDFFV-11228 remove arbitrary CMake warning groups.

* Make each flag a string

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

* Misc warning fixes (#495)

* Committing clang-format changes

* Misc warning fixes from Visual Studio

* Committing clang-format changes

* Fixes warnings in swmr.c test

* Committing clang-format changes

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

* Correct merge errors.

* Committing clang-format changes

Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
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>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>

6 files changed, 45 insertions, 42 deletions

diff --git a/c++/src/H5AbstractDs.h b/c++/src/H5AbstractDs.h
index cb43c73..b84867b 100644
--- a/c++/src/H5AbstractDs.h
+++ b/c++/src/H5AbstractDs.h
@@ -12,8 +12,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef AbstractDs_H
-#define AbstractDs_H
+#ifndef H5AbstractDs_H
+#define H5AbstractDs_H
 
 namespace H5 {
 
@@ -81,4 +81,4 @@ class H5_DLLCPP AbstractDs {
 }; // end of AbstractDs
 } // namespace H5
 
-#endif // AbstractDs_H
+#endif // H5AbstractDs_H
diff --git a/c++/src/H5CommonFG.h b/c++/src/H5CommonFG.h
index 368883b..d87f9ca 100644
--- a/c++/src/H5CommonFG.h
+++ b/c++/src/H5CommonFG.h
@@ -12,8 +12,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef CommonFG_H
-#define CommonFG_H
+#ifndef H5CommonFG_H
+#define H5CommonFG_H
 
 namespace H5 {
 
@@ -83,7 +83,7 @@ class H5_DLLCPP CommonFG {
 }; // end of CommonFG
 } // namespace H5
 
-#endif // CommonFG_H
+#endif // H5CommonFG_H
 
 /***************************************************************************
                                 Design Note
diff --git a/c++/src/H5Group.h b/c++/src/H5Group.h
index fb9fbe7..b5f7e51 100644
--- a/c++/src/H5Group.h
+++ b/c++/src/H5Group.h
@@ -12,8 +12,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef Group_H
-#define Group_H
+#ifndef H5Group_H
+#define H5Group_H
 
 namespace H5 {
 
@@ -83,4 +83,4 @@ class H5_DLLCPP Group : public H5Object, public CommonFG {
 }; // end of Group
 } // namespace H5
 
-#endif // Group_H
+#endif // H5Group_H
diff --git a/c++/src/H5IdComponent.h b/c++/src/H5IdComponent.h
index 4f75849..383d42d 100644
--- a/c++/src/H5IdComponent.h
+++ b/c++/src/H5IdComponent.h
@@ -12,8 +12,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef IdComponent_H
-#define IdComponent_H
+#ifndef H5IdComponent_H
+#define H5IdComponent_H
 
 namespace H5 {
 
@@ -113,4 +113,4 @@ class H5_DLLCPP IdComponent {
 }; // end class IdComponent
 } // namespace H5
 
-#endif // IdComponent_H
+#endif // H5IdComponent_H
diff --git a/c++/test/tarray.cpp b/c++/test/tarray.cpp
index ce1eae9..7525c5f 100644
--- a/c++/test/tarray.cpp
+++ b/c++/test/tarray.cpp
@@ -81,7 +81,7 @@ test_array_compound_array()
     // Initialize array data to write
     for (idxi = 0; idxi < SPACE1_DIM1; idxi++)
         for (idxj = 0; idxj < ARRAY1_DIM1; idxj++) {
-            wdata[idxi][idxj].i = idxi * 10 + idxj;
+            wdata[idxi][idxj].i = static_cast<int>(idxi * 10 + idxj);
             for (idxk = 0; idxk < ARRAY1_DIM1; idxk++) {
                 float temp                = idxi * 10.0 + idxj * 2.5 + idxk;
                 wdata[idxi][idxj].f[idxk] = temp;
@@ -178,8 +178,9 @@ test_array_compound_array()
         // Check the array dimensions
         for (ii = 0; ii < ndims; ii++)
             if (rdims1[ii] != tdims1[ii]) {
-                TestErrPrintf("Array dimension information doesn't match!, rdims1[%d]=%zd, tdims1[%d]=z%d\n",
-                              ii, rdims1[ii], ii, tdims1[ii]);
+                TestErrPrintf(
+                    "Array dimension information doesn't match!, rdims1[%d]=%lld, tdims1[%d]=%lld\n", ii,
+                    rdims1[ii], ii, tdims1[ii]);
                 continue;
             } // end if
 
@@ -196,8 +197,9 @@ test_array_compound_array()
         // Check the array dimensions
         for (ii = 0; ii < ndims; ii++)
             if (rdims1[ii] != tdims1[ii]) {
-                TestErrPrintf("Array dimension information doesn't match!, rdims1[%d]=%zd, tdims1[%d]=%zd\n",
-                              ii, rdims1[ii], ii, tdims1[ii]);
+                TestErrPrintf(
+                    "Array dimension information doesn't match!, rdims1[%d]=%lld, tdims1[%d]=%lld\n", ii,
+                    rdims1[ii], ii, tdims1[ii]);
                 continue;
             } // end if
 
@@ -246,8 +248,9 @@ test_array_compound_array()
         // Check the array dimensions
         for (ii = 0; ii < ndims; ii++)
             if (rdims1[ii] != tdims1[ii]) {
-                TestErrPrintf("Array dimension information doesn't match!, rdims1[%d]=%zd, tdims1[%d]=%zd\n",
-                              ii, rdims1[ii], ii, tdims1[ii]);
+                TestErrPrintf(
+                    "Array dimension information doesn't match!, rdims1[%d]=%lld, tdims1[%d]=%lld\n", ii,
+                    rdims1[ii], ii, tdims1[ii]);
                 continue;
             } // end if
 
@@ -262,9 +265,9 @@ test_array_compound_array()
         for (idxi = 0; idxi < SPACE1_DIM1; idxi++) {
             for (idxj = 0; idxj < ARRAY1_DIM1; idxj++) {
                 if (wdata[idxi][idxj].i != rdata[idxi][idxj].i) {
-                    TestErrPrintf(
-                        "Array data information doesn't match!, wdata[%d][%d].i=%d, rdata[%d][%d].i=%d\n",
-                        idxi, idxj, wdata[idxi][idxj].i, idxi, idxj, rdata[idxi][idxj].i);
+                    TestErrPrintf("Array data information doesn't match!, wdata[%lld][%lld].i=%d, "
+                                  "rdata[%lld][%lld].i=%d\n",
+                                  idxi, idxj, wdata[idxi][idxj].i, idxi, idxj, rdata[idxi][idxj].i);
                     continue;
                 } // end if
             }     // end for
@@ -383,7 +386,7 @@ test_array_info()
     // Initialize array data to write
     for (idxi = 0; idxi < SPACE1_DIM1; idxi++)
         for (idxj = 0; idxj < ARRAY1_DIM1; idxj++) {
-            wdata[idxi][idxj].i = idxi * 10 + idxj;
+            wdata[idxi][idxj].i = static_cast<int>(idxi * 10 + idxj);
             for (idxk = 0; idxk < ARRAY1_DIM1; idxk++) {
                 float temp                = idxi * 10.0 + idxj * 2.5 + idxk;
                 wdata[idxi][idxj].f[idxk] = temp;
@@ -455,7 +458,7 @@ test_array_info()
             for (ii = 0; ii < ndims; ii++)
                 if (rdims1[ii] != tdims1[ii]) {
                     TestErrPrintf(
-                        "Array dimension information doesn't match!, rdims1[%d]=%zd, tdims1[%d]=z%d\n", ii,
+                        "Array dimension information doesn't match!, rdims1[%d]=%llu, tdims1[%d]=z%llu\n", ii,
                         rdims1[ii], ii, tdims1[ii]);
                     continue;
                 } // end if
diff --git a/c++/test/tattr.cpp b/c++/test/tattr.cpp
index 85a1484..228b787 100644
--- a/c++/test/tattr.cpp
+++ b/c++/test/tattr.cpp
@@ -169,8 +169,8 @@ test_attr_basic_write()
         // Verify values read in
         for (i = 0; i < ATTR1_DIM1; i++)
             if (attr_data1[i] != read_data1[i])
-                TestErrPrintf("%d: attribute data different: attr_data1[%d]=%d,read_data1[%d]=%d\n", __LINE__,
-                              i, attr_data1[i], i, read_data1[i]);
+                TestErrPrintf("%d: attribute data different: attr_data1[%llu]=%d,read_data1[%llu]=%d\n",
+                              __LINE__, i, attr_data1[i], i, read_data1[i]);
 
         // Create two more attributes for this dataset, but only write to one.
         Attribute ds_attr2 = dataset.createAttribute(ATTR2_NAME, PredType::NATIVE_INT, att_space);
@@ -185,7 +185,7 @@ test_attr_basic_write()
         // Verify values read in
         for (i = 0; i < ATTR1_DIM1; i++)
             if (attr_data1a[i] != read_data1[i])
-                TestErrPrintf("%d: attribute data different: attr_data1a[%d]=%d,read_data1[%d]=%d\n",
+                TestErrPrintf("%d: attribute data different: attr_data1a[%llu]=%d,read_data1[%llu]=%d\n",
                               __LINE__, i, attr_data1a[i], i, read_data1[i]);
 
         // Close both attributes
@@ -448,8 +448,8 @@ test_attr_rename()
         // Verify values read in
         for (i = 0; i < ATTR1_DIM1; i++)
             if (attr_data1[i] != read_data1[i])
-                TestErrPrintf("%d: attribute data different: attr_data1[%d]=%d,read_data1[%d]=%d\n", __LINE__,
-                              i, attr_data1[i], i, read_data1[i]);
+                TestErrPrintf("%d: attribute data different: attr_data1[%llu]=%d,read_data1[%llu%d\n",
+                              __LINE__, i, attr_data1[i], i, read_data1[i]);
 
         // Close attribute
         attr1.close();
@@ -472,7 +472,7 @@ test_attr_rename()
         // Verify values read in
         for (i = 0; i < ATTR1_DIM1; i++)
             if (attr_data1a[i] != read_data1[i])
-                TestErrPrintf("%d: attribute data different: attr_data1a[%d]=%d,read_data1[%d]=%d\n",
+                TestErrPrintf("%d: attribute data different: attr_data1a[%llu]=%d,read_data1[%llu]=%d\n",
                               __LINE__, i, attr_data1a[i], i, read_data1[i]);
 
         // Close attribute
@@ -537,7 +537,7 @@ test_attr_basic_read()
         // Verify values read in
         for (i = 0; i < ATTR1_DIM1; i++)
             if (attr_data1[i] != read_data1[i])
-                TestErrPrintf("%d: attribute data different: attr_data1[%d]=%d, read_data1[%d]=%d\n",
+                TestErrPrintf("%d: attribute data different: attr_data1[%llu]=%d, read_data1[%llu]=%d\n",
                               __LINE__, i, attr_data1[i], i, read_data1[i]);
 
         /*
@@ -568,9 +568,9 @@ test_attr_basic_read()
         for (i = 0; i < ATTR2_DIM1; i++)
             for (j = 0; j < ATTR2_DIM2; j++)
                 if (attr_data2[i][j] != read_data2[i][j]) {
-                    TestErrPrintf(
-                        "%d: attribute data different: attr_data2[%d][%d]=%d, read_data2[%d][%d]=%d\n",
-                        __LINE__, i, j, attr_data2[i][j], i, j, read_data2[i][j]);
+                    TestErrPrintf("%d: attribute data different: attr_data2[%llu][%llu]=%d, "
+                                  "read_data2[%llu][%llu]=%d\n",
+                                  __LINE__, i, j, attr_data2[i][j], i, j, read_data2[i][j]);
                 }
         PASSED();
     } // end try block
@@ -1044,7 +1044,7 @@ test_attr_mult_read()
         hsize_t dims[ATTR_MAX_DIMS]; // Attribute dimensions
         int     ndims = space.getSimpleExtentDims(dims);
         if ((long)dims[0] != (long)ATTR1_DIM1)
-            TestErrPrintf("%d:attribute dimensions different: dims[0]=%d, should be %d\n", __LINE__,
+            TestErrPrintf("%d:attribute dimensions different: dims[0]=%d, should be %llu\n", __LINE__,
                           (int)dims[0], ATTR1_DIM1);
 
         /* Verify Datatype */
@@ -1072,8 +1072,8 @@ test_attr_mult_read()
         // Verify values read in
         for (i = 0; i < ATTR1_DIM1; i++)
             if (attr_data1[i] != read_data1[i])
-                TestErrPrintf("%d: attribute data different: attr_data1[%d]=%d,read_data1[%d]=%d\n", __LINE__,
-                              i, attr_data1[i], i, read_data1[i]);
+                TestErrPrintf("%d: attribute data different: attr_data1[%llu]=%d,read_data1[%llu]=%d\n",
+                              __LINE__, i, attr_data1[i], i, read_data1[i]);
 
         // Verify Name
         H5std_string attr_name = attr.getName();
@@ -1127,9 +1127,9 @@ test_attr_mult_read()
         for (i = 0; i < ATTR2_DIM1; i++)
             for (j = 0; j < ATTR2_DIM2; j++)
                 if (attr_data2[i][j] != read_data2[i][j])
-                    TestErrPrintf(
-                        "%d: attribute data different: attr_data2[%d][%d]=%d, read_data2[%d][%d]=%d\n",
-                        __LINE__, i, j, attr_data2[i][j], i, j, read_data2[i][j]);
+                    TestErrPrintf("%d: attribute data different: attr_data2[%llu][%llu]=%d, "
+                                  "read_data2[%llu][%llu]=%d\n",
+                                  __LINE__, i, j, attr_data2[i][j], i, j, read_data2[i][j]);
 
         // Verify Name
         attr_name = attr.getName();
@@ -1182,8 +1182,8 @@ test_attr_mult_read()
             for (j = 0; j < ATTR3_DIM2; j++)
                 for (k = 0; k < ATTR3_DIM3; k++)
                     if (attr_data3[i][j][k] != read_data3[i][j][k])
-                        TestErrPrintf("%d: attribute data different: attr_data3[%d][%d][%d]=%f, "
-                                      "read_data3[%d][%d][%d]=%f\n",
+                        TestErrPrintf("%d: attribute data different: attr_data3[%llu][%llu][%llu]=%f, "
+                                      "read_data3[%llu][%llu][%llu]=%f\n",
                                       __LINE__, i, j, k, attr_data3[i][j][k], i, j, k, read_data3[i][j][k]);
 
         // Verify Name