Hdf5 1 12 merge cmake ninja and java refs (#698)

* OESS-98 fix tools test for plugins

* sync fork

* Merge of changes from dev

* Move problem option to bottom of the list until fixed

* HDFFV-11106 - fix parsing optional args

* HDFFV-11106 add note

* grammer fix

* Whitespace after clang formatting

* Undo format version 11 changes

* Update check to working version

* Merge workflow and minor changes from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge serval small changes from dev

* fix typo

* Minor non-space formatting changes

* GH #386 copyright corrections for java folder

* revert because logic requires false return

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Remove case statement for H5I_EVENTSET

* Correct call with versioning

* Remove tabs

* Double underscore change

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
Remove more underscores from header guards

* Merge #380 from develop

* Correct date entry

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* Some Javadoc warning fixes

* Committing clang-format changes

* Updated javadoc fixes

* HDFFV-11228/9 merges from develop

* remove obsolete debug comment

* Fix conflict

* HDFFV-11229 merge changes from develop

* HDFFV-11229 merge second compare from develop

* HDFFV-11229 fix reference file

* HDFFV-11229 update autotools test script for two ref files

* HDFFV-11229 merge dev changes for long double display in tools

* Committing clang-format changes

* Update with changes from develop

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

Update pkgconfig scripts for parallel builds.
Fix install COPYING file reference.
Remove unused round defines.
Change CMake default setting of BUILD_CPP to off.

* Whitespace changes

* Rework CMake add_custom to use the BYPRODUCTS argument

* Revert CMake configure checks for round defines

* With VS 2015 minimum strdup is supported

* Doxygen comments merged from develop

* doxygen build updates

* Correct version string for map functions

* TRILAB-227 and tools debug merge from develop

* TRILAB-227 Enable test

* Quote subset args

* Use MATCHES in compiler id compare, merge from dev

* Revert test enable

* Add file to list

* doxygen version errors

* if blocks needed for build modes

* Update list of test platforms

* Issue #669 remove version from pkgcfg filename

* remove version from h5cc script

* Merge CMake and java refs from dev

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

.github/workflows/main.yml

@@ -36,7 +36,7 @@ jobs:
             os: ubuntu-latest
             build_type: "Release"
             cpp: ON
-            fortran: OFF
+            fortran: ON
             java: ON
             ts: OFF
             hl: ON

.github/workflows/pr-check.yml

@@ -31,7 +31,7 @@ jobs:
             os: ubuntu-latest
             build_type: "Release"
             cpp: ON
-            fortran: OFF
+            fortran: ON
             java: ON
             ts: OFF
             hl: ON

fortran/src/CMakeLists.txt

@@ -74,15 +74,15 @@ add_executable (H5match_types
 target_include_directories (H5match_types PRIVATE "${HDF5_SRC_BINARY_DIR};${HDF5_SRC_DIR};${HDF5_F90_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
 
 add_custom_command (TARGET H5match_types POST_BUILD
-    BYPRODUCTS H5f90i_gen.h H5fortran_types.F90
+    BYPRODUCTS ${HDF5_F90_BINARY_DIR}/H5f90i_gen.h ${HDF5_F90_BINARY_DIR}/H5fortran_types.F90
     COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:H5match_types>
     WORKING_DIRECTORY ${HDF5_F90_BINARY_DIR}
     DEPENDS H5match_types
 )
 
 if (NOT ONLY_SHARED_LIBS)
   add_custom_command (TARGET H5match_types POST_BUILD
-      BYPRODUCTS H5f90i_gen.h H5fortran_types.F90
+      BYPRODUCTS ${HDF5_F90_BINARY_DIR}/static/H5f90i_gen.h ${HDF5_F90_BINARY_DIR}/static/H5fortran_types.F90
       COMMAND    ${CMAKE_COMMAND}
       ARGS       -E copy_if_different ${HDF5_F90_BINARY_DIR}/H5f90i_gen.h ${HDF5_F90_BINARY_DIR}/static/H5f90i_gen.h
       COMMAND    ${CMAKE_COMMAND}
@@ -95,7 +95,7 @@ if (NOT ONLY_SHARED_LIBS)
 endif ()
 if (BUILD_SHARED_LIBS)
   add_custom_command (TARGET H5match_types POST_BUILD
-      BYPRODUCTS H5f90i_gen.h H5fortran_types.F90
+      BYPRODUCTS ${HDF5_F90_BINARY_DIR}/shared/H5f90i_gen.h ${HDF5_F90_BINARY_DIR}/shared/H5fortran_types.F90
       COMMAND    ${CMAKE_COMMAND}
       ARGS       -E copy_if_different ${HDF5_F90_BINARY_DIR}/H5f90i_gen.h ${HDF5_F90_BINARY_DIR}/shared/H5f90i_gen.h
       COMMAND    ${CMAKE_COMMAND}
@@ -235,7 +235,7 @@ add_custom_command (TARGET H5_buildiface POST_BUILD
 )
 if (NOT ONLY_SHARED_LIBS)
   add_custom_command (TARGET H5_buildiface POST_BUILD
-      BYPRODUCTS H5_gen.F90
+      BYPRODUCTS ${HDF5_F90_BINARY_DIR}/static/H5_gen.F90
       COMMAND    ${CMAKE_COMMAND}
       ARGS       -E copy_if_different ${HDF5_F90_BINARY_DIR}/H5_gen.F90 ${HDF5_F90_BINARY_DIR}/static/H5_gen.F90
       WORKING_DIRECTORY ${HDF5_F90_BINARY_DIR}/static
@@ -250,7 +250,7 @@ endif ()
 
 if (BUILD_SHARED_LIBS)
   add_custom_command (TARGET H5_buildiface POST_BUILD
-      BYPRODUCTS H5_gen.F90
+      BYPRODUCTS ${HDF5_F90_BINARY_DIR}/shared/H5_gen.F90
       COMMAND    ${CMAKE_COMMAND}
       ARGS       -E copy_if_different ${HDF5_F90_BINARY_DIR}/H5_gen.F90 ${HDF5_F90_BINARY_DIR}/shared/H5_gen.F90
       WORKING_DIRECTORY ${HDF5_F90_BINARY_DIR}/shared

fortran/test/CMakeLists.txt

@@ -92,7 +92,7 @@ endif ()
 
 if (NOT BUILD_SHARED_LIBS)
   add_custom_command (TARGET H5_test_buildiface POST_BUILD
-      BYPRODUCTS tf_gen.F90
+      BYPRODUCTS ${HDF5_FORTRAN_TESTS_BINARY_DIR}/static/tf_gen.F90
       COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:H5_test_buildiface>
       WORKING_DIRECTORY ${HDF5_FORTRAN_TESTS_BINARY_DIR}/static
       DEPENDS H5_test_buildiface
@@ -104,7 +104,7 @@ if (NOT BUILD_SHARED_LIBS)
   set_source_files_properties (${HDF5_FORTRAN_TESTS_BINARY_DIR}/static/tf_gen.F90 PROPERTIES GENERATED TRUE)
 else ()
   add_custom_command (TARGET H5_test_buildiface POST_BUILD
-      BYPRODUCTS tf_gen.F90
+      BYPRODUCTS ${HDF5_FORTRAN_TESTS_BINARY_DIR}/shared/tf_gen.F90
       COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:H5_test_buildiface>
       WORKING_DIRECTORY ${HDF5_FORTRAN_TESTS_BINARY_DIR}/shared
       DEPENDS H5_test_buildiface

hl/fortran/src/CMakeLists.txt

@@ -115,7 +115,7 @@ set (HDF5_HL_F90_F_BASE_SOURCES
 
 if (NOT ONLY_SHARED_LIBS)
   add_custom_command (TARGET H5HL_buildiface POST_BUILD
-      BYPRODUCTS $H5LTff_gen.F90 H5TBff_gen.F90
+      BYPRODUCTS ${HDF5_HL_F90_BINARY_DIR}/static/H5LTff_gen.F90 ${HDF5_HL_F90_BINARY_DIR}/static/H5TBff_gen.F90
       COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:H5HL_buildiface>
       WORKING_DIRECTORY ${HDF5_HL_F90_BINARY_DIR}/static
       DEPENDS ${HDF5_HL_F90_F_BASE_SOURCES}
@@ -132,7 +132,7 @@ if (NOT ONLY_SHARED_LIBS)
 endif ()
 if (BUILD_SHARED_LIBS)
   add_custom_command (TARGET H5HL_buildiface POST_BUILD
-      BYPRODUCTS H5LTff_gen.F90 H5TBff_gen.F90
+      BYPRODUCTS ${HDF5_HL_F90_BINARY_DIR}/shared/H5LTff_gen.F90 ${HDF5_HL_F90_BINARY_DIR}/shared/H5TBff_gen.F90
       COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:H5HL_buildiface>
       WORKING_DIRECTORY ${HDF5_HL_F90_BINARY_DIR}/shared
       DEPENDS ${HDF5_HL_F90_F_BASE_SOURCES}

java/src/hdf/hdf5lib/H5.java

@@ -10726,7 +10726,18 @@ public synchronized static native byte[] H5Rcopy(byte[] src_ref_ptr)
      * @exception IllegalArgumentException
      *                - an input array is invalid.
      **/
-    public synchronized static native long H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id)
+    public static long H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException {
+        long id = _H5Ropen_object(ref_ptr, rapl_id, oapl_id);
+        if (id > 0) {
+            log.trace("OPEN_IDS: H5Ropen_object add {}", id);
+            OPEN_IDS.add(id);
+            log.trace("OPEN_IDS: {}", OPEN_IDS.size());
+        }
+        return id;
+    }
+
+    private synchronized static native long _H5Ropen_object(byte[] ref_ptr, long rapl_id, long oapl_id)
             throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
     /**
@@ -10754,7 +10765,18 @@ public synchronized static native long H5Ropen_object(byte[] ref_ptr, long rapl_
      * @exception IllegalArgumentException
      *                - an input array is invalid.
      **/
-    public synchronized static native long H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id)
+    public static long H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException {
+        long id = _H5Ropen_region(ref_ptr, rapl_id, oapl_id);
+        if (id > 0) {
+            log.trace("OPEN_IDS: H5Ropen_region add {}", id);
+            OPEN_IDS.add(id);
+            log.trace("OPEN_IDS: {}", OPEN_IDS.size());
+        }
+        return id;
+    }
+
+    private synchronized static native long _H5Ropen_region(byte[] ref_ptr, long rapl_id, long oapl_id)
             throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
     /**
@@ -10782,7 +10804,18 @@ public synchronized static native long H5Ropen_region(byte[] ref_ptr, long rapl_
      * @exception IllegalArgumentException
      *                - an input array is invalid.
      **/
-    public synchronized static native long H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id)
+    public static long H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id)
+            throws HDF5LibraryException, NullPointerException, IllegalArgumentException {
+        long id = _H5Ropen_attr(ref_ptr, rapl_id, aapl_id);
+        if (id > 0) {
+            log.trace("OPEN_IDS: H5Ropen_attr add {}", id);
+            OPEN_IDS.add(id);
+            log.trace("OPEN_IDS: {}", OPEN_IDS.size());
+        }
+        return id;
+    }
+
+    private synchronized static native long _H5Ropen_attr(byte[] ref_ptr, long rapl_id, long aapl_id)
             throws HDF5LibraryException, NullPointerException, IllegalArgumentException;
 
     // Get type //

java/src/jni/h5rImp.c

@@ -336,7 +336,7 @@ Java_hdf_hdf5lib_H5_H5Rcopy(JNIEnv *env, jclass clss, jbyteArray src_ref)
  * Signature: ([BJJ)J
  */
 JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_H5_H5Ropen_1object(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id)
+Java_hdf_hdf5lib_H5__1H5Ropen_1object(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id)
 {
     jboolean isCopy;
     jbyte *  refBuf = NULL;
@@ -371,7 +371,7 @@ Java_hdf_hdf5lib_H5_H5Ropen_1object(JNIEnv *env, jclass clss, jbyteArray ref, jl
  * Signature: ([BJJ)J
  */
 JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_H5_H5Ropen_1region(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id)
+Java_hdf_hdf5lib_H5__1H5Ropen_1region(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong oapl_id)
 {
     jboolean isCopy;
     jbyte *  refBuf = NULL;
@@ -406,7 +406,7 @@ Java_hdf_hdf5lib_H5_H5Ropen_1region(JNIEnv *env, jclass clss, jbyteArray ref, jl
  * Signature: ([BJJ)J
  */
 JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_H5_H5Ropen_1attr(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong aapl_id)
+Java_hdf_hdf5lib_H5__1H5Ropen_1attr(JNIEnv *env, jclass clss, jbyteArray ref, jlong rapl_id, jlong aapl_id)
 {
     jboolean isCopy;
     jbyte *  refBuf = NULL;

java/src/jni/h5rImp.h

@@ -78,21 +78,21 @@ JNIEXPORT jbyteArray JNICALL Java_hdf_hdf5lib_H5_H5Rcopy(JNIEnv *, jclass, jbyte
  * Method:    H5Ropen_object
  * Signature: ([BJJ)J
  */
-JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Ropen_1object(JNIEnv *, jclass, jbyteArray, jlong, jlong);
+JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Ropen_1object(JNIEnv *, jclass, jbyteArray, jlong, jlong);
 
 /*
  * Class:     hdf_hdf5lib_H5
  * Method:    H5Ropen_region
  * Signature: ([BJJ)J
  */
-JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Ropen_1region(JNIEnv *, jclass, jbyteArray, jlong, jlong);
+JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Ropen_1region(JNIEnv *, jclass, jbyteArray, jlong, jlong);
 
 /*
  * Class:     hdf_hdf5lib_H5
  * Method:    H5Ropen_attr
  * Signature: ([BJJ)J
  */
-JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5_H5Ropen_1attr(JNIEnv *, jclass, jbyteArray, jlong, jlong);
+JNIEXPORT jlong JNICALL Java_hdf_hdf5lib_H5__1H5Ropen_1attr(JNIEnv *, jclass, jbyteArray, jlong, jlong);
 
 /*
  * Class:     hdf_hdf5lib_H5