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byrnHDFbyrnHDF
authored
1 10 Merges from develop (#424)
* HDFFV-10865 - merge from dev, HDFArray perf fix. * Remove duplicate setting * Whitespace changes after clang format * Undo version 11 clang format changes * Merge CMake changes from develop * test testing script merge from develop * Update supported platforms * PR#3 merge from develop * Merge gcc 10 diagnostics option from develop * Merge #318 OSX changes from develop * Merge small changes from develop * Minor non-space formatting changes * #386 copyright corrections for java folder * Merges from develop #358 patches from vtk #361 fix header guard spelling * Merge updates #358 patches from vtk #361 fix header guard spelling * format fix * Fix missing underscore and make H5public.h closer to dev * Merges from develop #340 clang -Wformat-security warnings #360 Fixed uninitialized warnings header guard underscore cleanup JNI cleanup * format alignment * Add missing test ref file
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‎MANIFEST

+2
Original file line numberDiff line numberDiff line change
@@ -1943,6 +1943,7 @@
19431943
./tools/testfiles/tintsnodata.h5
19441944
./tools/testfiles/tlarge_objname.ddl
19451945
./tools/testfiles/tlarge_objname.h5
1946+
./tools/testfiles/tldouble.ddl
19461947
./tools/testfiles/tldouble.h5
19471948
./tools/testfiles/tlonglinks.ddl
19481949
./tools/testfiles/tlonglinks.h5
@@ -2452,6 +2453,7 @@
24522453
./tools/test/h5diff/testfiles/h5diff_80.txt
24532454
./tools/test/h5diff/testfiles/h5diff_800.txt
24542455
./tools/test/h5diff/testfiles/h5diff_801.txt
2456+
./tools/test/h5diff/testfiles/h5diff_830.txt
24552457
./tools/test/h5diff/testfiles/h5diff_90.txt
24562458
./tools/test/h5diff/testfiles/h5diff_100.txt
24572459
./tools/test/h5diff/testfiles/h5diff_101.txt

‎c++/src/H5AbstractDs.h

+3-3
Original file line numberDiff line numberDiff line change
@@ -12,8 +12,8 @@
1212
* help@hdfgroup.org. *
1313
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
1414

15-
#ifndef __AbstractDs_H
16-
#define __AbstractDs_H
15+
#ifndef AbstractDs_H
16+
#define AbstractDs_H
1717

1818
namespace H5 {
1919

@@ -81,4 +81,4 @@ class H5_DLLCPP AbstractDs {
8181
}; // end of AbstractDs
8282
} // namespace H5
8383

84-
#endif // __AbstractDs_H
84+
#endif // AbstractDs_H

‎c++/src/H5CommonFG.h

+3-3
Original file line numberDiff line numberDiff line change
@@ -12,8 +12,8 @@
1212
* help@hdfgroup.org. *
1313
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
1414

15-
#ifndef __CommonFG_H
16-
#define __CommonFG_H
15+
#ifndef CommonFG_H
16+
#define CommonFG_H
1717

1818
namespace H5 {
1919

@@ -83,7 +83,7 @@ class H5_DLLCPP CommonFG {
8383
}; // end of CommonFG
8484
} // namespace H5
8585

86-
#endif // __CommonFG_H
86+
#endif // CommonFG_H
8787

8888
/***************************************************************************
8989
Design Note

‎c++/src/H5Group.h

+3-3
Original file line numberDiff line numberDiff line change
@@ -12,8 +12,8 @@
1212
* help@hdfgroup.org. *
1313
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
1414

15-
#ifndef __Group_H
16-
#define __Group_H
15+
#ifndef Group_H
16+
#define Group_H
1717

1818
namespace H5 {
1919

@@ -83,4 +83,4 @@ class H5_DLLCPP Group : public H5Object, public CommonFG {
8383
}; // end of Group
8484
} // namespace H5
8585

86-
#endif // __Group_H
86+
#endif // Group_H

‎c++/src/H5IdComponent.h

+3-3
Original file line numberDiff line numberDiff line change
@@ -12,8 +12,8 @@
1212
* help@hdfgroup.org. *
1313
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
1414

15-
#ifndef __IdComponent_H
16-
#define __IdComponent_H
15+
#ifndef IdComponent_H
16+
#define IdComponent_H
1717

1818
namespace H5 {
1919

@@ -113,4 +113,4 @@ class H5_DLLCPP IdComponent {
113113
}; // end class IdComponent
114114
} // namespace H5
115115

116-
#endif // __IdComponent_H
116+
#endif // IdComponent_H

‎config/gnu-cxxflags

+1-1
Original file line numberDiff line numberDiff line change
@@ -148,7 +148,7 @@ if test "X-g++" = "X-$cxx_vendor"; then
148148
# Enhanced Diagnostics #
149149
########################
150150

151-
if test $cc_vers_major -ge 10; then
151+
if test $cxx_vers_major -ge 10; then
152152
NO_DIAGS_CXXFLAGS="-fdiagnostics-urls=never -fno-diagnostics-color"
153153
fi
154154
DIAGS_CXXFLAGS=

‎config/gnu-fflags

+1-1
Original file line numberDiff line numberDiff line change
@@ -109,7 +109,7 @@ if test "X-gfortran" = "X-$f9x_vendor"; then
109109
# Enhanced Diagnostics #
110110
########################
111111

112-
if test $cc_vers_major -ge 10; then
112+
if test $f9x_vers_major -ge 10; then
113113
NO_DIAGS_FCFLAGS="-fdiagnostics-urls=never -fno-diagnostics-color"
114114
fi
115115
DIAGS_FCFLAGS=

‎fortran/src/H5match_types.c

+2-2
Original file line numberDiff line numberDiff line change
@@ -70,8 +70,8 @@ initCfile(void)
7070
* help@hdfgroup.org. *\n\
7171
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */\n\
7272
\n\n\
73-
#ifndef _H5f90i_gen_H\n\
74-
#define _H5f90i_gen_H\n\
73+
#ifndef H5f90i_gen_H\n\
74+
#define H5f90i_gen_H\n\
7575
\n\
7676
/* This file is automatically generated by H5match_types.c at build time. */\n\
7777
\n\

‎java/src/jni/exceptionImp.c

+23-10
Original file line numberDiff line numberDiff line change
@@ -262,11 +262,24 @@ H5JNIErrorClass(JNIEnv *env, const char *message, const char *className)
262262
* exception.
263263
*/
264264
jboolean
265-
h5outOfMemory(JNIEnv *env, const char *functName)
265+
h5outOfMemory(JNIEnv *env, const char *message)
266266
{
267-
return H5JNIErrorClass(env, functName, "java/lang/OutOfMemoryError");
267+
return H5JNIErrorClass(env, message, "java/lang/OutOfMemoryError");
268268
} /* end h5outOfMemory() */
269269

270+
/*
271+
* Create and throw an 'AssertionError'
272+
*
273+
* Note: This routine never returns from the 'throw',
274+
* and the Java native method immediately raises the
275+
* exception.
276+
*/
277+
jboolean
278+
h5assertion(JNIEnv *env, const char *message)
279+
{
280+
return H5JNIErrorClass(env, message, "java/lang/AssertionError");
281+
} /* end h5assertion() */
282+
270283
/*
271284
* A fatal error in a JNI call
272285
* Create and throw an 'InternalError'
@@ -276,9 +289,9 @@ h5outOfMemory(JNIEnv *env, const char *functName)
276289
* exception.
277290
*/
278291
jboolean
279-
h5JNIFatalError(JNIEnv *env, const char *functName)
292+
h5JNIFatalError(JNIEnv *env, const char *message)
280293
{
281-
return H5JNIErrorClass(env, functName, "java/lang/InternalError");
294+
return H5JNIErrorClass(env, message, "java/lang/InternalError");
282295
} /* end h5JNIFatalError() */
283296

284297
/*
@@ -290,9 +303,9 @@ h5JNIFatalError(JNIEnv *env, const char *functName)
290303
* exception.
291304
*/
292305
jboolean
293-
h5nullArgument(JNIEnv *env, const char *functName)
306+
h5nullArgument(JNIEnv *env, const char *message)
294307
{
295-
return H5JNIErrorClass(env, functName, "java/lang/NullPointerException");
308+
return H5JNIErrorClass(env, message, "java/lang/NullPointerException");
296309
} /* end h5nullArgument() */
297310

298311
/*
@@ -304,9 +317,9 @@ h5nullArgument(JNIEnv *env, const char *functName)
304317
* exception.
305318
*/
306319
jboolean
307-
h5badArgument(JNIEnv *env, const char *functName)
320+
h5badArgument(JNIEnv *env, const char *message)
308321
{
309-
return H5JNIErrorClass(env, functName, "java/lang/IllegalArgumentException");
322+
return H5JNIErrorClass(env, message, "java/lang/IllegalArgumentException");
310323
} /* end h5badArgument() */
311324

312325
/*
@@ -318,9 +331,9 @@ h5badArgument(JNIEnv *env, const char *functName)
318331
* exception.
319332
*/
320333
jboolean
321-
h5unimplemented(JNIEnv *env, const char *functName)
334+
h5unimplemented(JNIEnv *env, const char *message)
322335
{
323-
return H5JNIErrorClass(env, functName, "java/lang/UnsupportedOperationException");
336+
return H5JNIErrorClass(env, message, "java/lang/UnsupportedOperationException");
324337
} /* end h5unimplemented() */
325338

326339
/* h5raiseException(). This routine is called to generate

‎java/src/jni/exceptionImp.h

+3-3
Original file line numberDiff line numberDiff line change
@@ -13,8 +13,8 @@
1313
#include <jni.h>
1414
/* Header for class hdf_hdf5lib_H5_exception */
1515

16-
#ifndef _Included_hdf_hdf5lib_H5_exception
17-
#define _Included_hdf_hdf5lib_H5_exception
16+
#ifndef Included_hdf_hdf5lib_H5_exception
17+
#define Included_hdf_hdf5lib_H5_exception
1818

1919
#ifdef __cplusplus
2020
extern "C" {
@@ -67,4 +67,4 @@ JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_exceptions_HDF5LibraryException__1getMi
6767
} /* end extern "C" */
6868
#endif /* __cplusplus */
6969

70-
#endif /* _Included_hdf_hdf5lib_H5_exception */
70+
#endif /* Included_hdf_hdf5lib_H5_exception */

‎java/src/jni/h5Imp.h

+3-3
Original file line numberDiff line numberDiff line change
@@ -13,8 +13,8 @@
1313
#include <jni.h>
1414
/* Header for class hdf_hdf5lib_H5_H5 */
1515

16-
#ifndef _Included_hdf_hdf5lib_H5_H5
17-
#define _Included_hdf_hdf5lib_H5_H5
16+
#ifndef Included_hdf_hdf5lib_H5_H5
17+
#define Included_hdf_hdf5lib_H5_H5
1818

1919
#ifdef __cplusplus
2020
extern "C" {
@@ -82,4 +82,4 @@ JNIEXPORT jboolean JNICALL Java_hdf_hdf5lib_H5_H5is_1library_1threadsafe(JNIEnv
8282
} /* end extern "C" */
8383
#endif /* __cplusplus */
8484

85-
#endif /* _Included_hdf_hdf5lib_H5_H5 */
85+
#endif /* Included_hdf_hdf5lib_H5_H5 */

‎java/src/jni/h5aImp.c

+2-2
Original file line numberDiff line numberDiff line change
@@ -1133,7 +1133,7 @@ H5AreadVL_asstr(JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
11331133
for (i = 0; i < (size_t)n; i++) {
11341134
h5str.s[0] = '\0';
11351135

1136-
if (!h5str_sprintf(ENVONLY, &h5str, aid, tid, &(((char *)readBuf)[i * typeSize]), typeSize, 0))
1136+
if (!h5str_sprintf(ENVONLY, &h5str, aid, tid, &(((char *)readBuf)[i * typeSize]), 0))
11371137
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
11381138

11391139
if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, h5str.s)))
@@ -1425,7 +1425,7 @@ Java_hdf_hdf5lib_H5_H5Aread_1reg_1ref(JNIEnv *env, jclass clss, jlong attr_id, j
14251425
for (i = 0; i < n; i++) {
14261426
h5str.s[0] = '\0';
14271427

1428-
if (!h5str_sprintf(ENVONLY, &h5str, (hid_t)attr_id, (hid_t)mem_type_id, ref_data[i], 0, 0))
1428+
if (!h5str_sprintf(ENVONLY, &h5str, (hid_t)attr_id, (hid_t)mem_type_id, ref_data[i], 0))
14291429
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
14301430

14311431
if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, h5str.s)))

‎java/src/jni/h5aImp.h

+3-3
Original file line numberDiff line numberDiff line change
@@ -13,8 +13,8 @@
1313
#include <jni.h>
1414
/* Header for class hdf_hdf5lib_H5_H5A */
1515

16-
#ifndef _Included_hdf_hdf5lib_H5_H5A
17-
#define _Included_hdf_hdf5lib_H5_H5A
16+
#ifndef Included_hdf_hdf5lib_H5_H5A
17+
#define Included_hdf_hdf5lib_H5_H5A
1818

1919
#ifdef __cplusplus
2020
extern "C" {
@@ -375,4 +375,4 @@ JNIEXPORT jint JNICALL Java_hdf_hdf5lib_H5_H5Aiterate_1by_1name(JNIEnv *, jclass
375375
} /* end extern "C" */
376376
#endif /* __cplusplus */
377377

378-
#endif /* _Included_hdf_hdf5lib_H5_H5A */
378+
#endif /* Included_hdf_hdf5lib_H5_H5A */

‎java/src/jni/h5dImp.c

+2-2
Original file line numberDiff line numberDiff line change
@@ -1278,7 +1278,7 @@ H5DreadVL_asstr(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid
12781278
for (i = 0; i < (size_t)n; i++) {
12791279
h5str.s[0] = '\0';
12801280

1281-
if (!h5str_sprintf(ENVONLY, &h5str, did, tid, &(((char *)readBuf)[i * typeSize]), typeSize, 0))
1281+
if (!h5str_sprintf(ENVONLY, &h5str, did, tid, &(((char *)readBuf)[i * typeSize]), 0))
12821282
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
12831283

12841284
if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, h5str.s)))
@@ -1657,7 +1657,7 @@ Java_hdf_hdf5lib_H5_H5Dread_1reg_1ref(JNIEnv *env, jclass clss, jlong dataset_id
16571657
for (i = 0; i < n; i++) {
16581658
h5str.s[0] = '\0';
16591659

1660-
if (!h5str_sprintf(ENVONLY, &h5str, (hid_t)dataset_id, (hid_t)mem_type_id, &ref_data[i], 0, 0))
1660+
if (!h5str_sprintf(ENVONLY, &h5str, (hid_t)dataset_id, (hid_t)mem_type_id, &ref_data[i], 0))
16611661
CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
16621662

16631663
if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, h5str.s)))

‎java/src/jni/h5dImp.h

+3-3
Original file line numberDiff line numberDiff line change
@@ -13,8 +13,8 @@
1313
#include <jni.h>
1414
/* Header for class hdf_hdf5lib_H5_H5D */
1515

16-
#ifndef _Included_hdf_hdf5lib_H5_H5D
17-
#define _Included_hdf_hdf5lib_H5_H5D
16+
#ifndef Included_hdf_hdf5lib_H5_H5D
17+
#define Included_hdf_hdf5lib_H5_H5D
1818

1919
#ifdef __cplusplus
2020
extern "C" {
@@ -322,4 +322,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Drefresh(JNIEnv *, jclass, jlong);
322322
} /* end extern "C" */
323323
#endif /* __cplusplus */
324324

325-
#endif /* _Included_hdf_hdf5lib_H5_H5D */
325+
#endif /* Included_hdf_hdf5lib_H5_H5D */

‎java/src/jni/h5eImp.h

+3-3
Original file line numberDiff line numberDiff line change
@@ -13,8 +13,8 @@
1313
#include <jni.h>
1414
/* Header for class hdf_hdf5lib_H5_H5E */
1515

16-
#ifndef _Included_hdf_hdf5lib_H5_H5E
17-
#define _Included_hdf_hdf5lib_H5_H5E
16+
#ifndef Included_hdf_hdf5lib_H5_H5E
17+
#define Included_hdf_hdf5lib_H5_H5E
1818

1919
#ifdef __cplusplus
2020
extern "C" {
@@ -144,4 +144,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Ewalk2(JNIEnv *, jclass, jlong, jlo
144144
} /* end extern "C" */
145145
#endif /* __cplusplus */
146146

147-
#endif /* _Included_hdf_hdf5lib_H5_H5E */
147+
#endif /* Included_hdf_hdf5lib_H5_H5E */

‎java/src/jni/h5fImp.h

+3-3
Original file line numberDiff line numberDiff line change
@@ -13,8 +13,8 @@
1313
#include <jni.h>
1414
/* Header for class hdf_hdf5lib_H5_H5F */
1515

16-
#ifndef _Included_hdf_hdf5lib_H5_H5F
17-
#define _Included_hdf_hdf5lib_H5_H5F
16+
#ifndef Included_hdf_hdf5lib_H5_H5F
17+
#define Included_hdf_hdf5lib_H5_H5F
1818

1919
#ifdef __cplusplus
2020
extern "C" {
@@ -222,4 +222,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Fset_1libver_1bounds(JNIEnv *, jcla
222222
} /* end extern "C" */
223223
#endif /* __cplusplus */
224224

225-
#endif /* _Included_hdf_hdf5lib_H5_H5F */
225+
#endif /* Included_hdf_hdf5lib_H5_H5F */

‎java/src/jni/h5gImp.h

+3-3
Original file line numberDiff line numberDiff line change
@@ -13,8 +13,8 @@
1313
#include <jni.h>
1414
/* Header for class hdf_hdf5lib_H5_H5G */
1515

16-
#ifndef _Included_hdf_hdf5lib_H5_H5G
17-
#define _Included_hdf_hdf5lib_H5_H5G
16+
#ifndef Included_hdf_hdf5lib_H5_H5G
17+
#define Included_hdf_hdf5lib_H5_H5G
1818

1919
#ifdef __cplusplus
2020
extern "C" {
@@ -96,4 +96,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Grefresh(JNIEnv *, jclass, jlong);
9696
} /* end extern "C" */
9797
#endif /* __cplusplus */
9898

99-
#endif /* _Included_hdf_hdf5lib_H5_H5G */
99+
#endif /* Included_hdf_hdf5lib_H5_H5G */

‎java/src/jni/h5iImp.h

+3-3
Original file line numberDiff line numberDiff line change
@@ -13,8 +13,8 @@
1313
#include <jni.h>
1414
/* Header for class hdf_hdf5lib_H5_H5I */
1515

16-
#ifndef _Included_hdf_hdf5lib_H5_H5I
17-
#define _Included_hdf_hdf5lib_H5_H5I
16+
#ifndef Included_hdf_hdf5lib_H5_H5I
17+
#define Included_hdf_hdf5lib_H5_H5I
1818

1919
#ifdef __cplusplus
2020
extern "C" {
@@ -130,4 +130,4 @@ JNIEXPORT void JNICALL Java_hdf_hdf5lib_H5_H5Idestroy_1type(JNIEnv *, jclass, ji
130130
} /* end extern "C" */
131131
#endif /* __cplusplus */
132132

133-
#endif /* _Included_hdf_hdf5lib_H5_H5I */
133+
#endif /* Included_hdf_hdf5lib_H5_H5I */

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