Tools long double updates (#522)

* 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

* 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

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

1 files changed, 449 insertions, 0 deletions

diff --git a/java/test/TestH5Arw.java b/java/test/TestH5Arw.java
new file mode 100644
index 0000000..282b736
--- /dev/null
+++ b/java/test/TestH5Arw.java
@@ -0,0 +1,449 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+package test;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.File;
+
+import hdf.hdf5lib.H5;
+import hdf.hdf5lib.HDF5Constants;
+import hdf.hdf5lib.HDFNativeData;
+import hdf.hdf5lib.callbacks.H5A_iterate_cb;
+import hdf.hdf5lib.callbacks.H5A_iterate_t;
+import hdf.hdf5lib.exceptions.HDF5Exception;
+import hdf.hdf5lib.exceptions.HDF5LibraryException;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TestName;
+
+public class TestH5Arw {
+    @Rule public TestName testname = new TestName();
+    private static final String H5_INTS_FILE = "tintsattrs.h5";
+    private static final String H5_FLTS_FILE = "tfloatsattrs.h5";
+    private static final int DIM_X = 8;
+    private static final int DIM8_Y = 8;
+    private static final int DIM16_Y = 16;
+    private static final int DIM32_Y = 32;
+    private static final int DIM64_Y = 64;
+    private static final int DIM128_Y = 128;
+    private static final String DATASETU08 = "DU08BITS";
+    private static final String DATASETS08 = "DS08BITS";
+    private static final String DATASETU16 = "DU16BITS";
+    private static final String DATASETS16 = "DS16BITS";
+    private static final String DATASETU32 = "DU32BITS";
+    private static final String DATASETS32 = "DS32BITS";
+    private static final String DATASETU64 = "DU64BITS";
+    private static final String DATASETS64 = "DS64BITS";
+    private static final String DATASETF32 = "DS32BITS";
+    private static final String DATASETF64 = "DS64BITS";
+    private static final String DATASETF128 = "DS128BITS";
+    private static final int RANK = 2;
+    long H5fid = HDF5Constants.H5I_INVALID_HID;
+    long H5aid = HDF5Constants.H5I_INVALID_HID;
+    long H5did = HDF5Constants.H5I_INVALID_HID;
+
+    private final void _closeH5file() throws HDF5LibraryException {
+        if (H5aid >= 0)
+            try {H5.H5Aclose(H5aid);} catch (Exception ex) {}
+        if (H5did >= 0)
+            try {H5.H5Dclose(H5did);} catch (Exception ex) {}
+        if (H5fid > 0)
+            try {H5.H5Fclose(H5fid);} catch (Exception ex) {}
+    }
+
+    public void openH5file(String filename, String dsetname) {
+       try {
+           H5fid = H5.H5Fopen(filename,
+                   HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
+       }
+       catch (Throwable err) {
+           err.printStackTrace();
+           fail("TestH5Arw._openH5file: " + err);
+       }
+       assertTrue("TestH5Arw._openH5file: H5.H5Fopen: ", H5fid >= 0);
+       try {
+           H5did = H5.H5Dopen(H5fid, dsetname, HDF5Constants.H5P_DEFAULT);
+       }
+       catch (Throwable err) {
+           err.printStackTrace();
+           fail("TestH5Arw._openH5file: " + err);
+       }
+       assertTrue("TestH5Arw._openH5file: H5.H5Dopen: ", H5did >= 0);
+       try {
+           H5aid = H5.H5Aopen(H5did, dsetname, HDF5Constants.H5P_DEFAULT);
+       }
+       catch (Throwable err) {
+           err.printStackTrace();
+           fail("TestH5Arw._openH5file: " + err);
+       }
+       assertTrue("TestH5Arw._openH5file: H5.H5Aopen: ", H5aid >= 0);
+    }
+
+    @After
+    public void closeH5file() throws HDF5LibraryException {
+        if (H5aid >= 0)
+            try {H5.H5Aclose(H5aid);} catch (Exception ex) {}
+        if (H5did >= 0)
+            try {H5.H5Aclose(H5did);} catch (Exception ex) {}
+        if (H5fid > 0)
+            try {H5.H5Fclose(H5fid);} catch (Exception ex) {}
+        H5fid = HDF5Constants.H5I_INVALID_HID;
+        H5did = HDF5Constants.H5I_INVALID_HID;
+        H5aid = HDF5Constants.H5I_INVALID_HID;
+        System.out.println();
+    }
+
+    @Before
+    public void verifyCount()
+            throws NullPointerException, HDF5Exception {
+        assertTrue("H5 open ids is 0", H5.getOpenIDCount()==0);
+        System.out.print(testname.getMethodName());
+    }
+
+    @Test
+    public void testH5Aread_8bit_ints() {
+        byte[][] attr_data = new byte[DIM_X][DIM8_Y];
+
+        try {
+            openH5file(H5_INTS_FILE, DATASETU08);
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("testH5Aread_8bit_ints: openH5file: " + err);
+        }
+
+        // Read data.
+        try {
+            H5.H5Aread(H5aid, HDF5Constants.H5T_NATIVE_UINT8, attr_data);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_8bit_ints: H5Aread: " + err);
+        }
+
+        // End access to the attribute and release resources used by it.
+        try {
+            H5.H5Aclose(H5aid);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+        }
+
+        // End access to the dataset and release resources used by it.
+        try {
+            H5.H5Dclose(H5did);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+        }
+
+        // Open an existing dataset.
+        try {
+            H5did = H5.H5Dopen(H5fid, DATASETS08, HDF5Constants.H5P_DEFAULT);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_8bit_ints: H5Dopen: " + err);
+        }
+
+        // Open an existing attribute.
+        try {
+            H5aid = H5.H5Aopen(H5did, DATASETS08, HDF5Constants.H5P_DEFAULT);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_8bit_ints: H5Aopen: " + err);
+        }
+
+        // Read data.
+        try {
+            H5.H5Aread(H5aid, HDF5Constants.H5T_NATIVE_INT8, attr_data);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_8bit_ints: H5Aread: " + err);
+        }
+    }
+
+    @Test
+    public void testH5Aread_16bit_ints() {
+        short[][] attr_data = new short[DIM_X][DIM16_Y];
+
+        try {
+            openH5file(H5_INTS_FILE, DATASETU16);
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("testH5Aread_16bit_ints: openH5file: " + err);
+        }
+
+        // Read data.
+        try {
+            H5.H5Aread(H5aid, HDF5Constants.H5T_NATIVE_UINT16, attr_data);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_16bit_ints: H5Aread: " + err);
+        }
+
+        // End access to the attribute and release resources used by it.
+        try {
+            H5.H5Aclose(H5aid);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+        }
+
+        // End access to the dataset and release resources used by it.
+        try {
+            H5.H5Dclose(H5did);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+        }
+
+        // Open an existing dataset.
+        try {
+            H5did = H5.H5Dopen(H5fid, DATASETS16, HDF5Constants.H5P_DEFAULT);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_16bit_ints: H5Dopen: " + err);
+        }
+
+        // Open an existing attribute.
+        try {
+            H5aid = H5.H5Aopen(H5did, DATASETS16, HDF5Constants.H5P_DEFAULT);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_16bit_ints: H5Aopen: " + err);
+        }
+
+        // Read data.
+        try {
+            H5.H5Aread(H5aid, HDF5Constants.H5T_NATIVE_INT16, attr_data);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_16bit_ints: H5Aread: " + err);
+        }
+    }
+
+    @Test
+    public void testH5Aread_32bit_ints() {
+        int[][] attr_data = new int[DIM_X][DIM16_Y];
+
+        try {
+            openH5file(H5_INTS_FILE, DATASETU32);
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("testH5Aread_32bit_ints: openH5file: " + err);
+        }
+
+        // Read data.
+        try {
+            H5.H5Aread(H5aid, HDF5Constants.H5T_NATIVE_UINT32, attr_data);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_32bit_ints: H5Aread: " + err);
+        }
+
+        // End access to the attribute and release resources used by it.
+        try {
+            H5.H5Aclose(H5aid);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+        }
+
+        // End access to the dataset and release resources used by it.
+        try {
+            H5.H5Dclose(H5did);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+        }
+
+        // Open an existing dataset.
+        try {
+            H5did = H5.H5Dopen(H5fid, DATASETS32, HDF5Constants.H5P_DEFAULT);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_32bit_ints: H5Dopen: " + err);
+        }
+
+        // Open an existing attribute.
+        try {
+            H5aid = H5.H5Aopen(H5did, DATASETS32, HDF5Constants.H5P_DEFAULT);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_32bit_ints: H5Aopen: " + err);
+        }
+
+        // Read data.
+        try {
+            H5.H5Aread(H5aid, HDF5Constants.H5T_NATIVE_INT32, attr_data);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_32bit_ints: H5Aread: " + err);
+        }
+    }
+
+    @Test
+    public void testH5Aread_64bit_ints() {
+        long[][] attr_data = new long[DIM_X][DIM64_Y];
+
+        try {
+            openH5file(H5_INTS_FILE, DATASETU64);
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("testH5Aread_64bit_ints: openH5file: " + err);
+        }
+
+        // Read data.
+        try {
+            H5.H5Aread(H5aid, HDF5Constants.H5T_NATIVE_UINT64, attr_data);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_64bit_ints: H5Aread: " + err);
+        }
+
+        // End access to the attribute and release resources used by it.
+        try {
+            H5.H5Aclose(H5aid);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+        }
+
+        // End access to the dataset and release resources used by it.
+        try {
+            H5.H5Dclose(H5did);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+        }
+
+        // Open an existing dataset.
+        try {
+            H5did = H5.H5Dopen(H5fid, DATASETS64, HDF5Constants.H5P_DEFAULT);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_64bit_ints: H5Dopen: " + err);
+        }
+
+        // Open an existing attribute.
+        try {
+            H5aid = H5.H5Aopen(H5did, DATASETS64, HDF5Constants.H5P_DEFAULT);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_64bit_ints: H5Aopen: " + err);
+        }
+
+        // Read data.
+        try {
+            H5.H5Aread(H5aid, HDF5Constants.H5T_NATIVE_INT64, attr_data);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_64bit_ints: H5Aread: " + err);
+        }
+    }
+
+    @Test
+    public void testH5Aread_32bit_floats() {
+        float[][] attr_data = new float[DIM_X][DIM32_Y];
+
+        try {
+            openH5file(H5_FLTS_FILE, DATASETF32);
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("testH5Aread_32bit_floats: openH5file: " + err);
+        }
+
+        // Read data.
+        try {
+            H5.H5Aread(H5aid, HDF5Constants.H5T_NATIVE_FLOAT, attr_data);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_32bit_floats: H5Aread: " + err);
+        }
+        for (int i = 0; i < DIM_X; i++)
+            assertTrue("testH5Aread_32bit_floats - H5.H5Aread: ", attr_data[i][0] == (32 - i));
+    }
+
+    @Test
+    public void testH5Aread_64bit_floats() {
+        double[][] attr_data = new double[DIM_X][DIM64_Y];
+
+        try {
+            openH5file(H5_FLTS_FILE, DATASETF64);
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("testH5Aread_64bit_floats: openH5file: " + err);
+        }
+
+        // Read data.
+        try {
+            H5.H5Aread(H5aid, HDF5Constants.H5T_NATIVE_DOUBLE, attr_data);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_64bit_floats: H5Aread: " + err);
+        }
+        for (int i = 0; i < DIM_X; i++)
+            assertTrue("testH5Aread_64bit_floats - H5.H5Aread: ", attr_data[i][0] == (64 - i));
+    }
+
+    @Test
+    public void testH5Aread_128bit_floats() {
+        byte[][][] attr_data = new byte[DIM_X][DIM128_Y][8];
+
+        try {
+            openH5file(H5_FLTS_FILE, DATASETF128);
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("testH5Aread_128bit_floats: openH5file: " + err);
+        }
+
+        // Read data.
+        try {
+            H5.H5Aread(H5aid, HDF5Constants.H5T_NATIVE_LDOUBLE, attr_data);
+        }
+        catch (Exception err) {
+            err.printStackTrace();
+            fail("testH5Aread_128bit_floats: H5Aread: " + err);
+        }
+    }
+
+}