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, 41 insertions, 26 deletions

diff --git a/java/test/TestH5Pfapls3.java b/java/test/TestH5Pfapls3.java
index dda2716..06baef2 100644
--- a/java/test/TestH5Pfapls3.java
+++ b/java/test/TestH5Pfapls3.java
@@ -31,12 +31,13 @@ import org.junit.Test;
 import org.junit.rules.TestName;
 
 public class TestH5Pfapls3 {
-    @Rule public TestName testname = new TestName();
+    @Rule
+    public TestName testname = new TestName();
 
-    long fapl_id = HDF5Constants.H5I_INVALID_HID;
-    long plapl_id = HDF5Constants.H5I_INVALID_HID;
-    long dapl_id = HDF5Constants.H5I_INVALID_HID;
-    long plist_id = HDF5Constants.H5I_INVALID_HID;
+    long fapl_id    = HDF5Constants.H5I_INVALID_HID;
+    long plapl_id   = HDF5Constants.H5I_INVALID_HID;
+    long dapl_id    = HDF5Constants.H5I_INVALID_HID;
+    long plist_id   = HDF5Constants.H5I_INVALID_HID;
     long btplist_id = HDF5Constants.H5I_INVALID_HID;
 
     @Before
@@ -62,9 +63,9 @@ public class TestH5Pfapls3 {
         }
         assertTrue(plapl_id > 0);
         try {
-            plist_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_XFER);
+            plist_id   = H5.H5Pcreate(HDF5Constants.H5P_DATASET_XFER);
             btplist_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_XFER);
-            dapl_id = H5.H5Pcreate(HDF5Constants.H5P_DATASET_ACCESS);
+            dapl_id    = H5.H5Pcreate(HDF5Constants.H5P_DATASET_ACCESS);
         }
         catch (Throwable err) {
             err.printStackTrace();
@@ -79,15 +80,35 @@ public class TestH5Pfapls3 {
     public void deleteFileAccess() throws HDF5LibraryException
     {
         if (fapl_id > 0)
-            try {H5.H5Pclose(fapl_id);} catch (Exception ex) {}
+            try {
+                H5.H5Pclose(fapl_id);
+            }
+            catch (Exception ex) {
+            }
         if (plapl_id > 0)
-            try {H5.H5Pclose(plapl_id);} catch (Exception ex) {}
+            try {
+                H5.H5Pclose(plapl_id);
+            }
+            catch (Exception ex) {
+            }
         if (dapl_id > 0)
-            try {H5.H5Pclose(dapl_id);} catch (Exception ex) {}
+            try {
+                H5.H5Pclose(dapl_id);
+            }
+            catch (Exception ex) {
+            }
         if (plist_id > 0)
-            try {H5.H5Pclose(plist_id);} catch (Exception ex) {}
+            try {
+                H5.H5Pclose(plist_id);
+            }
+            catch (Exception ex) {
+            }
         if (btplist_id > 0)
-            try {H5.H5Pclose(btplist_id);} catch (Exception ex) {}
+            try {
+                H5.H5Pclose(btplist_id);
+            }
+            catch (Exception ex) {
+            }
         System.out.println();
     }
 
@@ -98,18 +119,15 @@ public class TestH5Pfapls3 {
             return;
 
         final H5FD_ros3_fapl_t config = new H5FD_ros3_fapl_t();
-        assertEquals("Default fapl has unexpected contents",
-                new H5FD_ros3_fapl_t("", "", ""), config);
+        assertEquals("Default fapl has unexpected contents", new H5FD_ros3_fapl_t("", "", ""), config);
 
         H5.H5Pset_fapl_ros3(fapl_id, config);
 
-        assertEquals("driver types don't match",
-                HDF5Constants.H5FD_ROS3, H5.H5Pget_driver(fapl_id));
+        assertEquals("driver types don't match", HDF5Constants.H5FD_ROS3, H5.H5Pget_driver(fapl_id));
 
         /* get_fapl_ros3 can throw exception in error cases */
         H5FD_ros3_fapl_t copy = H5.H5Pget_fapl_ros3(fapl_id);
-        assertEquals("contents of fapl set and get don't match",
-                new H5FD_ros3_fapl_t("", "", ""), copy);
+        assertEquals("contents of fapl set and get don't match", new H5FD_ros3_fapl_t("", "", ""), copy);
     }
 
     @Test(expected = HDF5LibraryException.class)
@@ -125,13 +143,12 @@ public class TestH5Pfapls3 {
     {
         if (HDF5Constants.H5FD_ROS3 < 0)
             throw new HDF5LibraryException("skip");
-        if (HDF5Constants.H5FD_SEC2 < 0 )
+        if (HDF5Constants.H5FD_SEC2 < 0)
             throw new HDF5LibraryException("skip");
-            /* TODO: for now, test against a sec2 fapl only */
+        /* TODO: for now, test against a sec2 fapl only */
 
         H5.H5Pset_fapl_sec2(fapl_id);
-        assertEquals("fapl_id was not set properly",
-                HDF5Constants.H5FD_SEC2, H5.H5Pget_driver(fapl_id));
+        assertEquals("fapl_id was not set properly", HDF5Constants.H5FD_SEC2, H5.H5Pget_driver(fapl_id));
         H5FD_ros3_fapl_t fails = H5.H5Pget_fapl_ros3(fapl_id);
     }
 
@@ -147,12 +164,10 @@ public class TestH5Pfapls3 {
 
         final H5FD_ros3_fapl_t config = new H5FD_ros3_fapl_t(region, acc_id, acc_key);
         H5.H5Pset_fapl_ros3(fapl_id, config);
-        assertEquals("driver types don't match",
-                HDF5Constants.H5FD_ROS3, H5.H5Pget_driver(fapl_id));
+        assertEquals("driver types don't match", HDF5Constants.H5FD_ROS3, H5.H5Pget_driver(fapl_id));
 
         H5FD_ros3_fapl_t copy = H5.H5Pget_fapl_ros3(fapl_id);
         assertEquals("contents of fapl set and get don't match",
-                new H5FD_ros3_fapl_t(region, acc_id, acc_key), copy);
+                     new H5FD_ros3_fapl_t(region, acc_id, acc_key), copy);
     }
-
 }