Onion VFD: Sync with develop (#1685)

* Removes unused definitions from module headers (#1624)

* Fix these Doxygen warnings #1581 (#1589)

* Fixes a typo in H5.c (#1639)

* free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638)

* free MPI_Group/MPI_Comm/MPI_Datatype objects

* fix clang-format style

* Adds build and license shields to README.md (#1641)

* First stab at a Github status bar

* Adds a .tokeignore file for counting lines of code accurately

* Yanks lines of code calculation since it wildly overcounts

* not depend on doIO to free an MPI_Comm object (#1642)

* free MPI datatypes previously created (#1637)

* Retrieve MPI-IO hints used by MPI library after file open (#1636)

H5Pget_fapl_mpio() should return an MPI info object containing all the
MPI-IO hints used by the MPI library underneath, after the file is
opened. Some hints, such as cb_nodes (number of I/O aggregators), are
useful for HDF5 applications and I/O libraries built on top of HDF5.

* OESS-168: Remove clang warnings. (#1309)

* OESS-168: Remove clang warnings.

* OESS-168: Address @lrknox review.

* OESS-168: Remove clang warnings. (#1376)

* Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426)

* Do not conditionally compile code that uses a pointer dereference
and assignment to copy a potentially unaligned variable to aligned
automatic storage, or vice versa.  Instead, always use naked `memcpy(3)`s.
Disassembling the generated code reveals that the `memcpy(3)`s optimize
(`-O3`) to a single `mov` instruction for x86_64, which is not strict
about alignment.

This change reduces the size of code and scripts by 143 lines, eases
our way to cross-compilation, and avoids invoking undefined behavior.

* Committing clang-format changes

* Per discussion, use HD and add comments.

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

* Cleans up some HL library code that inappropriately returns htri_t values cast to herr_t (#1651)

* Cleans up some HL library code that inappropriately returns
htri_t values cast to herr_t

* Committing clang-format changes

* Formatted source

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

* Mirror vfd test fixes (#1629)

* Use the FAPL that was created earlier in the test (and delete an unused
variable).   This allows 'make check-vfd' to pass with --enable-mirror-vfd.

* Check for testing directory before creating, to avoid warning from bash.
Clean out .libs directory before re-using it (after a failed test), to
remove any files generated by libtool.

* Committing clang-format changes

* Increment error count on failed file open and skip tests for VFDs that need
modified filenames.

* Skip the mirror VFD for 'make check-vfd' - the mirror VFD requires networking
configuration parameters and can't be provided for an automated test that
is configured with an environment variable.

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

* Removes HDF Group paths, adds shellcheck fixes (#1656)

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2230 -- which is non-standard. Use builti...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

* HDFFV-11306 Fixed (#1657)

* HDFFV-11306,
 * Fixed it so both h5open_f and h5close_f can be called multiple times.
 * Fixed an issue with open objects remaining after h5close_f was called.
 * Added additional tests.

* comments clean-up

* Develop clang format java (#1653)

* added HDFFV-11306 entry (#1662)

* Adds the -q flag to all swmr test programs, quieting noisy output (#1665)

* Adds paths-ignore to the Github pull request workflow (#1663)

* Changes Github action `hdf5 dev CI` to `PR hdf5 dev CI` (#1666)

So the PR action name is not the same as the one in main.yml

* Replace H5detect's build-time detection of C99 integer properties with a (#1400)

* Replace H5detect's build-time detection of C99 integer properties with a
table-driven routine, `H5T__init_native_int()`, that is run at library
initialization time.

* Improve handling of copying of dynamic libraries and clean them up after (#1681)

test finishes.

Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Wei-keng Liao <wkliao@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Quincey Koziol <koziol@lbl.gov>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>

1 files changed, 26 insertions, 25 deletions

diff --git a/java/examples/datatypes/H5Ex_T_Float.java b/java/examples/datatypes/H5Ex_T_Float.java
index e8da7f6..9ca099e 100644
--- a/java/examples/datatypes/H5Ex_T_Float.java
+++ b/java/examples/datatypes/H5Ex_T_Float.java
@@ -28,17 +28,18 @@ import hdf.hdf5lib.H5;
 import hdf.hdf5lib.HDF5Constants;
 
 public class H5Ex_T_Float {
-    private static String FILENAME = "H5Ex_T_Float.h5";
+    private static String FILENAME    = "H5Ex_T_Float.h5";
     private static String DATASETNAME = "DS1";
-    private static final int DIM0 = 4;
-    private static final int DIM1 = 7;
-    private static final int RANK = 2;
-
-    private static void CreateDataset() {
-        long file_id = HDF5Constants.H5I_INVALID_HID;
-        long dataspace_id = HDF5Constants.H5I_INVALID_HID;
-        long dataset_id = HDF5Constants.H5I_INVALID_HID;
-        long[] dims = { DIM0, DIM1 };
+    private static final int DIM0     = 4;
+    private static final int DIM1     = 7;
+    private static final int RANK     = 2;
+
+    private static void CreateDataset()
+    {
+        long file_id         = HDF5Constants.H5I_INVALID_HID;
+        long dataspace_id    = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id      = HDF5Constants.H5I_INVALID_HID;
+        long[] dims          = {DIM0, DIM1};
         double[][] dset_data = new double[DIM0][DIM1];
 
         // Initialize data.
@@ -50,7 +51,7 @@ public class H5Ex_T_Float {
         // Create a new file using default properties.
         try {
             file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
-                    HDF5Constants.H5P_DEFAULT);
+                                   HDF5Constants.H5P_DEFAULT);
         }
         catch (Exception e) {
             e.printStackTrace();
@@ -73,7 +74,8 @@ public class H5Ex_T_Float {
         try {
             if ((file_id >= 0) && (dataspace_id >= 0))
                 dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_IEEE_F64LE, dataspace_id,
-                        HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
+                                          HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT,
+                                          HDF5Constants.H5P_DEFAULT);
         }
         catch (Exception e) {
             e.printStackTrace();
@@ -82,8 +84,8 @@ public class H5Ex_T_Float {
         // Write the data to the dataset.
         try {
             if (dataset_id >= 0)
-                H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
-                        HDF5Constants.H5P_DEFAULT, dset_data);
+                H5.H5Dwrite(dataset_id, HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5S_ALL,
+                            HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data);
         }
         catch (Exception e) {
             e.printStackTrace();
@@ -115,14 +117,14 @@ public class H5Ex_T_Float {
         catch (Exception e) {
             e.printStackTrace();
         }
-
     }
 
-    private static void ReadDataset() {
-        long file_id = HDF5Constants.H5I_INVALID_HID;
+    private static void ReadDataset()
+    {
+        long file_id      = HDF5Constants.H5I_INVALID_HID;
         long dataspace_id = HDF5Constants.H5I_INVALID_HID;
-        long dataset_id = HDF5Constants.H5I_INVALID_HID;
-        long[] dims = { DIM0, DIM1 };
+        long dataset_id   = HDF5Constants.H5I_INVALID_HID;
+        long[] dims       = {DIM0, DIM1};
         double[][] dset_data;
 
         // Open an existing file.
@@ -161,13 +163,13 @@ public class H5Ex_T_Float {
 
         // Allocate array of pointers to two-dimensional arrays (the
         // elements of the dataset.
-        dset_data = new double[(int) dims[0]][(int) (dims[1])];
+        dset_data = new double[(int)dims[0]][(int)(dims[1])];
 
         // Read data.
         try {
             if (dataset_id >= 0)
-                H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
-                        HDF5Constants.H5P_DEFAULT, dset_data);
+                H5.H5Dread(dataset_id, HDF5Constants.H5T_NATIVE_DOUBLE, HDF5Constants.H5S_ALL,
+                           HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, dset_data);
         }
         catch (Exception e) {
             e.printStackTrace();
@@ -211,10 +213,10 @@ public class H5Ex_T_Float {
         catch (Exception e) {
             e.printStackTrace();
         }
-
     }
 
-    public static void main(String[] args) {
+    public static void main(String[] args)
+    {
         H5Ex_T_Float.CreateDataset();
         // Now we begin the read section of this example. Here we assume
         // the dataset and array have the same name and rank, but can have
@@ -222,5 +224,4 @@ public class H5Ex_T_Float {
         // data using malloc().
         H5Ex_T_Float.ReadDataset();
     }
-
 }