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
HDFGroup · Mar 4, 2021 · 583e9d5 · 583e9d5
1 parent 7b23ce1
commit 583e9d5
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Showing 133 changed files with 1,132 additions and 956 deletions.
diff --git a/MANIFEST b/MANIFEST
@@ -1943,6 +1943,7 @@
 ./tools/testfiles/tintsnodata.h5
 ./tools/testfiles/tlarge_objname.ddl
 ./tools/testfiles/tlarge_objname.h5
+./tools/testfiles/tldouble.ddl
 ./tools/testfiles/tldouble.h5
 ./tools/testfiles/tlonglinks.ddl
 ./tools/testfiles/tlonglinks.h5
@@ -2452,6 +2453,7 @@
 ./tools/test/h5diff/testfiles/h5diff_80.txt
 ./tools/test/h5diff/testfiles/h5diff_800.txt
 ./tools/test/h5diff/testfiles/h5diff_801.txt
+./tools/test/h5diff/testfiles/h5diff_830.txt
 ./tools/test/h5diff/testfiles/h5diff_90.txt
 ./tools/test/h5diff/testfiles/h5diff_100.txt
 ./tools/test/h5diff/testfiles/h5diff_101.txt

diff --git a/c++/src/H5AbstractDs.h b/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
diff --git a/c++/src/H5CommonFG.h b/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

diff --git a/c++/src/H5Group.h b/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
diff --git a/c++/src/H5IdComponent.h b/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
diff --git a/config/gnu-cxxflags b/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=

diff --git a/config/gnu-fflags b/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=

diff --git a/fortran/src/H5match_types.c b/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\

diff --git a/java/src/jni/exceptionImp.c b/java/src/jni/exceptionImp.c
@@ -262,11 +262,24 @@ H5JNIErrorClass(JNIEnv *env, const char *message, const char *className)
  *  exception.
  */
 jboolean
-h5outOfMemory(JNIEnv *env, const char *functName)
+h5outOfMemory(JNIEnv *env, const char *message)
 {
-    return H5JNIErrorClass(env, functName, "java/lang/OutOfMemoryError");
+    return H5JNIErrorClass(env, message, "java/lang/OutOfMemoryError");
 } /* end h5outOfMemory() */
 
+/*
+ *  Create and throw an 'AssertionError'
+ *
+ *  Note:  This routine never returns from the 'throw',
+ *  and the Java native method immediately raises the
+ *  exception.
+ */
+jboolean
+h5assertion(JNIEnv *env, const char *message)
+{
+    return H5JNIErrorClass(env, message, "java/lang/AssertionError");
+} /* end h5assertion() */
+
 /*
  *  A fatal error in a JNI call
  *  Create and throw an 'InternalError'
@@ -276,9 +289,9 @@ h5outOfMemory(JNIEnv *env, const char *functName)
  *  exception.
  */
 jboolean
-h5JNIFatalError(JNIEnv *env, const char *functName)
+h5JNIFatalError(JNIEnv *env, const char *message)
 {
-    return H5JNIErrorClass(env, functName, "java/lang/InternalError");
+    return H5JNIErrorClass(env, message, "java/lang/InternalError");
 } /* end h5JNIFatalError() */
 
 /*
@@ -290,9 +303,9 @@ h5JNIFatalError(JNIEnv *env, const char *functName)
  *  exception.
  */
 jboolean
-h5nullArgument(JNIEnv *env, const char *functName)
+h5nullArgument(JNIEnv *env, const char *message)
 {
-    return H5JNIErrorClass(env, functName, "java/lang/NullPointerException");
+    return H5JNIErrorClass(env, message, "java/lang/NullPointerException");
 } /* end h5nullArgument() */
 
 /*
@@ -304,9 +317,9 @@ h5nullArgument(JNIEnv *env, const char *functName)
  *  exception.
  */
 jboolean
-h5badArgument(JNIEnv *env, const char *functName)
+h5badArgument(JNIEnv *env, const char *message)
 {
-    return H5JNIErrorClass(env, functName, "java/lang/IllegalArgumentException");
+    return H5JNIErrorClass(env, message, "java/lang/IllegalArgumentException");
 } /* end h5badArgument() */
 
 /*
@@ -318,9 +331,9 @@ h5badArgument(JNIEnv *env, const char *functName)
  *  exception.
  */
 jboolean
-h5unimplemented(JNIEnv *env, const char *functName)
+h5unimplemented(JNIEnv *env, const char *message)
 {
-    return H5JNIErrorClass(env, functName, "java/lang/UnsupportedOperationException");
+    return H5JNIErrorClass(env, message, "java/lang/UnsupportedOperationException");
 } /* end h5unimplemented() */
 
 /*  h5raiseException().  This routine is called to generate

diff --git a/java/src/jni/exceptionImp.h b/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 */
diff --git a/java/src/jni/h5Imp.h b/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 */
diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c
@@ -1133,7 +1133,7 @@ H5AreadVL_asstr(JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
     for (i = 0; i < (size_t)n; i++) {
         h5str.s[0] = '\0';
 
-        if (!h5str_sprintf(ENVONLY, &h5str, aid, tid, &(((char *)readBuf)[i * typeSize]), typeSize, 0))
+        if (!h5str_sprintf(ENVONLY, &h5str, aid, tid, &(((char *)readBuf)[i * typeSize]), 0))
             CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
 
         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
     for (i = 0; i < n; i++) {
         h5str.s[0] = '\0';
 
-        if (!h5str_sprintf(ENVONLY, &h5str, (hid_t)attr_id, (hid_t)mem_type_id, ref_data[i], 0, 0))
+        if (!h5str_sprintf(ENVONLY, &h5str, (hid_t)attr_id, (hid_t)mem_type_id, ref_data[i], 0))
             CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
 
         if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, h5str.s)))

diff --git a/java/src/jni/h5aImp.h b/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 */
diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c
@@ -1278,7 +1278,7 @@ H5DreadVL_asstr(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid
     for (i = 0; i < (size_t)n; i++) {
         h5str.s[0] = '\0';
 
-        if (!h5str_sprintf(ENVONLY, &h5str, did, tid, &(((char *)readBuf)[i * typeSize]), typeSize, 0))
+        if (!h5str_sprintf(ENVONLY, &h5str, did, tid, &(((char *)readBuf)[i * typeSize]), 0))
             CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
 
         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
     for (i = 0; i < n; i++) {
         h5str.s[0] = '\0';
 
-        if (!h5str_sprintf(ENVONLY, &h5str, (hid_t)dataset_id, (hid_t)mem_type_id, &ref_data[i], 0, 0))
+        if (!h5str_sprintf(ENVONLY, &h5str, (hid_t)dataset_id, (hid_t)mem_type_id, &ref_data[i], 0))
             CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
 
         if (NULL == (jstr = ENVPTR->NewStringUTF(ENVONLY, h5str.s)))

diff --git a/java/src/jni/h5dImp.h b/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 */
diff --git a/java/src/jni/h5eImp.h b/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 */
diff --git a/java/src/jni/h5fImp.h b/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" {
@@ -222,4 +222,4 @@ 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 */
diff --git a/java/src/jni/h5gImp.h b/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 */
diff --git a/java/src/jni/h5iImp.h b/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 */