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Java and fortran cmake changes (HDFGroup#694)
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* 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 HDFGroup#386 java folder copyright corrections

* Whitespace

* GH HDFGroup#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 HDFGroup#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

* Some Javadoc warning fixes

* Updated javadoc fixes

* # WARNING: head commit changed in the meantime

HDFFV-11229 Fix long double usage in tools and java

Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.

* Committing clang-format changes

* HDFFV-11229 Add release note

* HDFFV-11229 windows testfile needed

* fix typo

* Remove non supported message text

* HDFFV-11229 - change ldouble test to check both native and general

* HDFFV-11229 add second file compare

* HDFFV-11229 fix reference file

* HDFFV-11229 autotools check two refs

* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output

* Committing clang-format changes

* Update release note

* Update attribute type of ref file

* Change source of ninja for macs

* try port instead of brew

* Recommended is to use brew.

* Undo non long double changes

* remove unneeded file

* Fix perl and doxygen CMake code

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

* Add stamp files to BYPRODUCTS

* Only one copy of file exists

* Fix custom cmmand depends targets

* Fix fortran custom command DEPENDS

* Add LD_LIBRARY_PATH to tests

* Add custom target for DEPENDS

* Add h5detect conditionaly to generated target DEPENDS

* Correct DEPENDS targets

* Parallel builds need the mpi compiler for pkgconfig scripts.

* install only if MPI build

* Fortran target depends

* Remove incorrect source attribute

* doxygen adjustments

* doxygen build updates

* Correct version

* Correct function version - function has been merged to 1.12

* Correct version string for map functions

* Cleanup warnings for tools debug builds

* TRILAB-227 - fix indexing for h5diff selections

* Correct location of pos to index function call

* TRILAB-227 Enable test

* Quote subset args

* Use MATCHES because of AppleClang

* if blocks needed for build modes

* Update list of DT platforms

* VS2019 correctly displays float values

* revert VS2019 change

* Issue HDFGroup#669 remove version from pkgcfg filename

* remove version from h5cc script

* Java reference functions updated

enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging

* Correct BYPRODUCTS argument

* Correct more genereated files BYPRODUCTS

* BYPRODUCTS must have unique locations

* Fix typo

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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@derobins @github-actions
derobins and github-actions[bot] committed May 30, 2021
1 parent 9973f96 commit f4be95c
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Showing 9 changed files with 122 additions and 87 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/main.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ jobs:
os: ubuntu-latest
build_type: "Release"
cpp: ON
fortran: OFF
fortran: ON
java: ON
ts: OFF
hl: ON
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2 changes: 1 addition & 1 deletion .github/workflows/pr-check.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ jobs:
os: ubuntu-latest
build_type: "Release"
cpp: ON
fortran: OFF
fortran: ON
java: ON
ts: OFF
hl: ON
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10 changes: 5 additions & 5 deletions fortran/src/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -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}
Expand All @@ -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}
Expand Down Expand Up @@ -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
Expand All @@ -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
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4 changes: 2 additions & 2 deletions fortran/test/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -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 ${HDF5_FORTRAN_TESTS_BINARY_DIR}/static
DEPENDS H5_test_buildiface
Expand All @@ -104,7 +104,7 @@ if (NOT BUILD_SHARED_LIBS)
set_source_files_properties (${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
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4 changes: 2 additions & 2 deletions hl/fortran/src/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -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}
Expand All @@ -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}
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39 changes: 36 additions & 3 deletions java/src/hdf/hdf5lib/H5.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;

/**
Expand Down Expand Up @@ -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;

/**
Expand Down Expand Up @@ -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 //
Expand Down
6 changes: 3 additions & 3 deletions java/src/jni/h5rImp.c
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand Down
6 changes: 3 additions & 3 deletions java/src/jni/h5rImp.h
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
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