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

c++/src/H5AbstractDs.h

@@ -12,8 +12,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef __AbstractDs_H
-#define __AbstractDs_H
+#ifndef AbstractDs_H
+#define AbstractDs_H
 
 namespace H5 {
 
@@ -81,4 +81,4 @@ class H5_DLLCPP AbstractDs {
 }; // end of AbstractDs
 } // namespace H5
 
-#endif // __AbstractDs_H
+#endif // AbstractDs_H

c++/src/H5CommonFG.h

@@ -12,8 +12,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef __CommonFG_H
-#define __CommonFG_H
+#ifndef CommonFG_H
+#define CommonFG_H
 
 namespace H5 {
 
@@ -83,7 +83,7 @@ class H5_DLLCPP CommonFG {
 }; // end of CommonFG
 } // namespace H5
 
-#endif // __CommonFG_H
+#endif // CommonFG_H
 
 /***************************************************************************
                                 Design Note

c++/src/H5Group.h

@@ -12,8 +12,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef __Group_H
-#define __Group_H
+#ifndef Group_H
+#define Group_H
 
 namespace H5 {
 
@@ -83,4 +83,4 @@ class H5_DLLCPP Group : public H5Object, public CommonFG {
 }; // end of Group
 } // namespace H5
 
-#endif // __Group_H
+#endif // Group_H

c++/src/H5IdComponent.h

@@ -12,8 +12,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef __IdComponent_H
-#define __IdComponent_H
+#ifndef IdComponent_H
+#define IdComponent_H
 
 namespace H5 {
 
@@ -113,4 +113,4 @@ class H5_DLLCPP IdComponent {
 }; // end class IdComponent
 } // namespace H5
 
-#endif // __IdComponent_H
+#endif // IdComponent_H

config/cmake/HDF5PluginCache.cmake

@@ -20,7 +20,7 @@ set (HDF5_REPACK_EXECUTABLE $<TARGET_FILE:h5repack-shared> CACHE STRING "hdf5 h5
 
 set (H5PL_ALLOW_EXTERNAL_SUPPORT "${HDF5_ALLOW_EXTERNAL_SUPPORT}" CACHE STRING "Allow External Library Building (NO GIT TGZ)" FORCE)
 
-set (H5PL_GIT_URL "https://git@bitbucket.hdfgroup.org/scm/test/h5plugin.git" CACHE STRING "Use plugins from HDF repository" FORCE)
+set (H5PL_GIT_URL "https://github.com/HDFGroup/hdf5_plugins.git" CACHE STRING "Use plugins from HDF repository" FORCE)
 set (H5PL_GIT_BRANCH "master" CACHE STRING "" FORCE)
 
 set (H5PL_TGZ_NAME "${PLUGIN_TGZ_NAME}" CACHE STRING "Use plugins from compressed file" FORCE)

config/gnu-cxxflags

@@ -148,7 +148,7 @@ if test "X-g++" = "X-$cxx_vendor"; then
     # Enhanced Diagnostics #
     ########################
 
-    if test $cc_vers_major -ge 10; then
+    if test $cxx_vers_major -ge 10; then
         NO_DIAGS_CXXFLAGS="-fdiagnostics-urls=never -fno-diagnostics-color"
     fi
     DIAGS_CXXFLAGS=

config/gnu-fflags

@@ -109,7 +109,7 @@ if test "X-gfortran" = "X-$f9x_vendor"; then
     # Enhanced Diagnostics #
     ########################
 
-    if test $cc_vers_major -ge 10; then
+    if test $f9x_vers_major -ge 10; then
         NO_DIAGS_FCFLAGS="-fdiagnostics-urls=never -fno-diagnostics-color"
     fi
     DIAGS_FCFLAGS=

fortran/src/H5match_types.c

@@ -70,8 +70,8 @@ initCfile(void)
  * help@hdfgroup.org.                                                        *\n\
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */\n\
 \n\n\
-#ifndef _H5f90i_gen_H\n\
-#define _H5f90i_gen_H\n\
+#ifndef H5f90i_gen_H\n\
+#define H5f90i_gen_H\n\
 \n\
 /* This file is automatically generated by H5match_types.c at build time. */\n\
 \n\

hl/src/hdf5_hl.h

@@ -17,8 +17,9 @@
  * fill this file with lots of gunk...
  */
 
-#ifndef _HDF5_HL_H
-#define _HDF5_HL_H
+#ifndef HDF5_HL_H
+#define HDF5_HL_H
+
 #include "hdf5.h"       /* hdf5 main library */
 #include "H5DOpublic.h" /* dataset optimization */
 #include "H5DSpublic.h" /* dimension scales */
@@ -28,4 +29,4 @@
 #include "H5PTpublic.h" /* packet table */
 #include "H5LDpublic.h" /* lite dataset */
 
-#endif /*H5_INCLUDE_HL*/
+#endif /*HDF5_HL_H*/

java/src/jni/exceptionImp.h

@@ -13,8 +13,8 @@
 #include <jni.h>
 /* Header for class hdf_hdf5lib_H5_exception */
 
-#ifndef _Included_hdf_hdf5lib_H5_exception
-#define _Included_hdf_hdf5lib_H5_exception
+#ifndef Included_hdf_hdf5lib_H5_exception
+#define Included_hdf_hdf5lib_H5_exception
 
 #ifdef __cplusplus
 extern "C" {
@@ -67,4 +67,4 @@ JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_exceptions_HDF5LibraryException__1getMi
 } /* end extern "C" */
 #endif /* __cplusplus */
 
-#endif /* _Included_hdf_hdf5lib_H5_exception */
+#endif /* Included_hdf_hdf5lib_H5_exception */

java/src/jni/h5Imp.h

@@ -13,8 +13,8 @@
 #include <jni.h>
 /* Header for class hdf_hdf5lib_H5_H5 */
 
-#ifndef _Included_hdf_hdf5lib_H5_H5
-#define _Included_hdf_hdf5lib_H5_H5
+#ifndef Included_hdf_hdf5lib_H5_H5
+#define Included_hdf_hdf5lib_H5_H5
 
 #ifdef __cplusplus
 extern "C" {
@@ -82,4 +82,4 @@ JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5is_1library_1threadsafe(JNIEnv
 } /* end extern "C" */
 #endif /* __cplusplus */
 
-#endif /* _Included_hdf_hdf5lib_H5_H5 */
+#endif /* Included_hdf_hdf5lib_H5_H5 */

java/src/jni/h5aImp.h

@@ -13,8 +13,8 @@
 #include <jni.h>
 /* Header for class hdf_hdf5lib_H5_H5A */
 
-#ifndef _Included_hdf_hdf5lib_H5_H5A
-#define _Included_hdf_hdf5lib_H5_H5A
+#ifndef Included_hdf_hdf5lib_H5_H5A
+#define Included_hdf_hdf5lib_H5_H5A
 
 #ifdef __cplusplus
 extern "C" {
@@ -375,4 +375,4 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Aiterate_1by_1name(JNIEnv *, jclass
 } /* end extern "C" */
 #endif /* __cplusplus */
 
-#endif /* _Included_hdf_hdf5lib_H5_H5A */
+#endif /* Included_hdf_hdf5lib_H5_H5A */

java/src/jni/h5dImp.h

@@ -13,8 +13,8 @@
 #include <jni.h>
 /* Header for class hdf_hdf5lib_H5_H5D */
 
-#ifndef _Included_hdf_hdf5lib_H5_H5D
-#define _Included_hdf_hdf5lib_H5_H5D
+#ifndef Included_hdf_hdf5lib_H5_H5D
+#define Included_hdf_hdf5lib_H5_H5D
 
 #ifdef __cplusplus
 extern "C" {
@@ -322,4 +322,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Drefresh(JNIEnv *, jclass, jlong);
 } /* end extern "C" */
 #endif /* __cplusplus */
 
-#endif /* _Included_hdf_hdf5lib_H5_H5D */
+#endif /* Included_hdf_hdf5lib_H5_H5D */

java/src/jni/h5eImp.h

@@ -13,8 +13,8 @@
 #include <jni.h>
 /* Header for class hdf_hdf5lib_H5_H5E */
 
-#ifndef _Included_hdf_hdf5lib_H5_H5E
-#define _Included_hdf_hdf5lib_H5_H5E
+#ifndef Included_hdf_hdf5lib_H5_H5E
+#define Included_hdf_hdf5lib_H5_H5E
 
 #ifdef __cplusplus
 extern "C" {
@@ -144,4 +144,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Ewalk2(JNIEnv *, jclass, jlong, jlo
 } /* end extern "C" */
 #endif /* __cplusplus */
 
-#endif /* _Included_hdf_hdf5lib_H5_H5E */
+#endif /* Included_hdf_hdf5lib_H5_H5E */

java/src/jni/h5fImp.h

@@ -13,8 +13,8 @@
 #include <jni.h>
 /* Header for class hdf_hdf5lib_H5_H5F */
 
-#ifndef _Included_hdf_hdf5lib_H5_H5F
-#define _Included_hdf_hdf5lib_H5_H5F
+#ifndef Included_hdf_hdf5lib_H5_H5F
+#define Included_hdf_hdf5lib_H5_H5F
 
 #ifdef __cplusplus
 extern "C" {
@@ -236,4 +236,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Fset_1libver_1bounds(JNIEnv *, jcla
 } /* end extern "C" */
 #endif /* __cplusplus */
 
-#endif /* _Included_hdf_hdf5lib_H5_H5F */
+#endif /* Included_hdf_hdf5lib_H5_H5F */

java/src/jni/h5gImp.h

@@ -13,8 +13,8 @@
 #include <jni.h>
 /* Header for class hdf_hdf5lib_H5_H5G */
 
-#ifndef _Included_hdf_hdf5lib_H5_H5G
-#define _Included_hdf_hdf5lib_H5_H5G
+#ifndef Included_hdf_hdf5lib_H5_H5G
+#define Included_hdf_hdf5lib_H5_H5G
 
 #ifdef __cplusplus
 extern "C" {
@@ -96,4 +96,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Grefresh(JNIEnv *, jclass, jlong);
 } /* end extern "C" */
 #endif /* __cplusplus */
 
-#endif /* _Included_hdf_hdf5lib_H5_H5G */
+#endif /* Included_hdf_hdf5lib_H5_H5G */

java/src/jni/h5iImp.h

@@ -13,8 +13,8 @@
 #include <jni.h>
 /* Header for class hdf_hdf5lib_H5_H5I */
 
-#ifndef _Included_hdf_hdf5lib_H5_H5I
-#define _Included_hdf_hdf5lib_H5_H5I
+#ifndef Included_hdf_hdf5lib_H5_H5I
+#define Included_hdf_hdf5lib_H5_H5I
 
 #ifdef __cplusplus
 extern "C" {
@@ -130,4 +130,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Idestroy_1type(JNIEnv *, jclass, ji
 } /* end extern "C" */
 #endif /* __cplusplus */
 
-#endif /* _Included_hdf_hdf5lib_H5_H5I */
+#endif /* Included_hdf_hdf5lib_H5_H5I */

java/src/jni/h5jni.h

@@ -21,8 +21,8 @@
 #include <string.h>
 #include "H5private.h"
 
-#ifndef _Included_h5jni
-#define _Included_h5jni
+#ifndef Included_h5jni
+#define Included_h5jni
 
 #ifdef __cplusplus
 #define ENVPTR (env)
@@ -344,4 +344,4 @@ extern jobject create_H5O_token_t(JNIEnv *env, const H5O_token_t *token, hbool_t
 } /* end extern "C" */
 #endif /* __cplusplus */
 
-#endif /* _Included_h5jni */
+#endif /* Included_h5jni */

java/src/jni/h5lImp.h

@@ -13,8 +13,8 @@
 #include <jni.h>
 /* Header for class hdf_hdf5lib_H5_H5_H5L */
 
-#ifndef _Included_hdf_hdf5lib_H5_H5L
-#define _Included_hdf_hdf5lib_H5_H5L
+#ifndef Included_hdf_hdf5lib_H5_H5L
+#define Included_hdf_hdf5lib_H5_H5L
 
 #ifdef __cplusplus
 extern "C" {
@@ -170,4 +170,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Lunregister(JNIEnv *, jclass, jint)
 } /* end extern "C" */
 #endif /* __cplusplus */
 
-#endif /* _Included_hdf_hdf5lib_H5_H5L */
+#endif /* Included_hdf_hdf5lib_H5_H5L */

java/src/jni/h5oImp.h

@@ -13,8 +13,8 @@
 #include <jni.h>
 /* Header for class hdf_hdf5lib_H5_H5_H5O */
 
-#ifndef _Included_hdf_hdf5lib_H5_H5O
-#define _Included_hdf_hdf5lib_H5_H5O
+#ifndef Included_hdf_hdf5lib_H5_H5O
+#define Included_hdf_hdf5lib_H5_H5O
 
 #ifdef __cplusplus
 extern "C" {
@@ -217,4 +217,4 @@ JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5Oare_1mdc_1flushes_1disabled(JN
 } /* end extern "C" */
 #endif /* __cplusplus */
 
-#endif /* _Included_hdf_hdf5lib_H5_H5O */
+#endif /* Included_hdf_hdf5lib_H5_H5O */

java/src/jni/h5pACPLImp.h

@@ -10,8 +10,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef _Included_hdf_hdf5lib_H5_H5PACPL
-#define _Included_hdf_hdf5lib_H5_H5PACPL
+#ifndef Included_hdf_hdf5lib_H5_H5PACPL
+#define Included_hdf_hdf5lib_H5_H5PACPL
 
 #include <jni.h>
 
@@ -23,4 +23,4 @@ extern "C" {
 } /* end extern "C" */
 #endif /* __cplusplus */
 
-#endif /* _Included_hdf_hdf5lib_H5_H5PACPL */
+#endif /* Included_hdf_hdf5lib_H5_H5PACPL */

java/src/jni/h5pDAPLImp.h

@@ -10,8 +10,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef _Included_hdf_hdf5lib_H5_H5PDAPL
-#define _Included_hdf_hdf5lib_H5_H5PDAPL
+#ifndef Included_hdf_hdf5lib_H5_H5PDAPL
+#define Included_hdf_hdf5lib_H5_H5PDAPL
 
 #include <jni.h>
 
@@ -93,4 +93,4 @@ JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Pget_1virtual_1printf_1gap(JNIEnv
 } /* end extern "C" */
 #endif /* __cplusplus */
 
-#endif /* _Included_hdf_hdf5lib_H5_H5PDAPL */
+#endif /* Included_hdf_hdf5lib_H5_H5PDAPL */

java/src/jni/h5pDCPLImp.h

@@ -10,8 +10,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef _Included_hdf_hdf5lib_H5_H5PDCPL
-#define _Included_hdf_hdf5lib_H5_H5PDCPL
+#ifndef Included_hdf_hdf5lib_H5_H5PDCPL
+#define Included_hdf_hdf5lib_H5_H5PDCPL
 
 #include <jni.h>
 
@@ -320,4 +320,4 @@ JNIEXPORT jstring JNICALL Java_hdf_hdf5lib_H5_H5Pget_1virtual_1prefix(JNIEnv *,
 } /* end extern "C" */
 #endif /* __cplusplus */
 
-#endif /* _Included_hdf_hdf5lib_H5_H5PDCPL */
+#endif /* Included_hdf_hdf5lib_H5_H5PDCPL */

java/src/jni/h5pDXPLImp.h

@@ -10,8 +10,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef _Included_hdf_hdf5lib_H5_H5PDXPL
-#define _Included_hdf_hdf5lib_H5_H5PDXPL
+#ifndef Included_hdf_hdf5lib_H5_H5PDXPL
+#define Included_hdf_hdf5lib_H5_H5PDXPL
 
 #include <jni.h>
 
@@ -181,4 +181,4 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Pget_1btree_1ratios(JNIEnv *, jclas
 } /* end extern "C" */
 #endif /* __cplusplus */
 
-#endif /* _Included_hdf_hdf5lib_H5_H5PDXPL */
+#endif /* Included_hdf_hdf5lib_H5_H5PDXPL */

java/src/jni/h5pFAPLImp.h

@@ -10,8 +10,8 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-#ifndef _Included_hdf_hdf5lib_H5_H5PFAPL
-#define _Included_hdf_hdf5lib_H5_H5PFAPL
+#ifndef Included_hdf_hdf5lib_H5_H5PFAPL
+#define Included_hdf_hdf5lib_H5_H5PFAPL
 
 #include <jni.h>
 
@@ -476,4 +476,4 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Pget_1libver_1bounds(JNIEnv *, jcla
 } /* end extern "C" */
 #endif /* __cplusplus */
 
-#endif /* _Included_hdf_hdf5lib_H5_H5PFAPL */
+#endif /* Included_hdf_hdf5lib_H5_H5PFAPL */