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, 97 insertions, 64 deletions

diff --git a/java/test/TestH5Edefault.java b/java/test/TestH5Edefault.java
index 9e93cea..c412cf2 100644
--- a/java/test/TestH5Edefault.java
+++ b/java/test/TestH5Edefault.java
@@ -15,25 +15,28 @@ package test;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
+
 import hdf.hdf5lib.H5;
 import hdf.hdf5lib.HDF5Constants;
 import hdf.hdf5lib.exceptions.HDF5LibraryException;
 
 import org.junit.After;
 import org.junit.Before;
+import org.junit.Ignore;
 import org.junit.Rule;
 import org.junit.Test;
-import org.junit.Ignore;
 import org.junit.rules.TestName;
 
 public class TestH5Edefault {
-    @Rule public TestName testname = new TestName();
+    @Rule
+    public TestName testname = new TestName();
 
     public static final int ERRSTACK_CNT = 6;
 
     @Before
-    public void H5Eset_default_stack() {
-        assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0);
+    public void H5Eset_default_stack()
+    {
+        assertTrue("H5 open ids is 0", H5.getOpenIDCount() == 0);
         System.out.print(testname.getMethodName());
 
         try {
@@ -46,23 +49,26 @@ public class TestH5Edefault {
         }
     }
     @After
-    public void nextTestName() {
+    public void nextTestName()
+    {
         System.out.println();
     }
 
     @Test(expected = IllegalArgumentException.class)
-    public void testH5Eprint2_invalid_classid() throws Throwable {
+    public void testH5Eprint2_invalid_classid() throws Throwable
+    {
         H5.H5Eprint2(-1, null);
     }
 
     @Ignore
-    public void testH5Eprint() {
+    public void testH5Eprint()
+    {
         /*
-        * If HDF5_VOL_CONNECTOR is set, this might not be the
-        * native connector and the error stack might be different.
-        * Only check for the specific error stack if the native
-        * connector is being used.
-        */
+         * If HDF5_VOL_CONNECTOR is set, this might not be the
+         * native connector and the error stack might be different.
+         * Only check for the specific error stack if the native
+         * connector is being used.
+         */
         String connector = System.getenv("HDF5_VOL_CONNECTOR");
         if (connector == null) {
             try {
@@ -81,19 +87,20 @@ public class TestH5Edefault {
     }
 
     @Test
-    public void testH5Eget_current_stack() {
-        long num_msg = -1;
-        long num_msg_default = -1;
-        long saved_num_msg = -1;
-        long stack_id = -1;
+    public void testH5Eget_current_stack()
+    {
+        long num_msg          = -1;
+        long num_msg_default  = -1;
+        long saved_num_msg    = -1;
+        long stack_id         = -1;
         long stack_id_default = HDF5Constants.H5E_DEFAULT;
         try {
             H5.H5Fopen("test", HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
         }
         catch (Throwable err) {
-            //default stack id will be different after exception
+            // default stack id will be different after exception
             stack_id_default = HDF5Constants.H5E_DEFAULT;
-            //err.printStackTrace(); //This will clear the error stack
+            // err.printStackTrace(); //This will clear the error stack
         }
         // Verify we have messages on the error stack
         try {
@@ -147,16 +154,17 @@ public class TestH5Edefault {
     }
 
     @Test
-    public void testH5Eget_current_stack_pop() {
-        long num_msg = -1;
+    public void testH5Eget_current_stack_pop()
+    {
+        long num_msg         = -1;
         long num_msg_default = -1;
-        long saved_num_msg = -1;
-        long stack_id = -1;
+        long saved_num_msg   = -1;
+        long stack_id        = -1;
         try {
             H5.H5Fopen("test", HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
         }
         catch (Throwable err) {
-            //err.printStackTrace(); //This will clear the error stack
+            // err.printStackTrace(); //This will clear the error stack
         }
 
         // Verify there are error messages on the stack and save it
@@ -179,7 +187,8 @@ public class TestH5Edefault {
             fail("H5.H5Eget_current_stack: " + err);
         }
         assertFalse("H5.H5Eget_current_stack: get_current_stack - " + stack_id, stack_id < 0);
-        assertFalse("H5.H5Eget_current_stack: get_current_stack - " + stack_id, stack_id == HDF5Constants.H5E_DEFAULT);
+        assertFalse("H5.H5Eget_current_stack: get_current_stack - " + stack_id,
+                    stack_id == HDF5Constants.H5E_DEFAULT);
 
         // Verify the stack is empty
         try {
@@ -206,7 +215,7 @@ public class TestH5Edefault {
             H5.H5Fopen("test", HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
         }
         catch (Throwable err) {
-            //err.printStackTrace(); //This will clear the error stack
+            // err.printStackTrace(); //This will clear the error stack
         }
 
         // Verify we have a nonzero number of messages and save it
@@ -243,37 +252,44 @@ public class TestH5Edefault {
     }
 
     @Test(expected = IllegalArgumentException.class)
-    public void testH5Eclose_stack_invalid_stackid() throws Throwable {
+    public void testH5Eclose_stack_invalid_stackid() throws Throwable
+    {
         H5.H5Eclose_stack(-1);
     }
 
     @Test(expected = IllegalArgumentException.class)
-    public void testH5Eget_class_name_invalid_classid() throws Throwable {
+    public void testH5Eget_class_name_invalid_classid() throws Throwable
+    {
         H5.H5Eget_class_name(-1);
     }
 
     @Test(expected = HDF5LibraryException.class)
-    public void testH5Eget_class_name_invalid_classname() throws Throwable {
+    public void testH5Eget_class_name_invalid_classname() throws Throwable
+    {
         H5.H5Eget_class_name(HDF5Constants.H5E_DEFAULT);
     }
 
     @Test(expected = IllegalArgumentException.class)
-    public void testH5Eclose_msg_invalid_errid() throws Throwable {
+    public void testH5Eclose_msg_invalid_errid() throws Throwable
+    {
         H5.H5Eclose_msg(-1);
     }
 
     @Test(expected = IllegalArgumentException.class)
-    public void testH5Ecreate_msg_invalid_errid() throws Throwable {
+    public void testH5Ecreate_msg_invalid_errid() throws Throwable
+    {
         H5.H5Ecreate_msg(-1, HDF5Constants.H5E_MAJOR, "null");
     }
 
     @Test(expected = IllegalArgumentException.class)
-    public void testH5Eget_msg_invalid_msgid() throws Throwable {
+    public void testH5Eget_msg_invalid_msgid() throws Throwable
+    {
         H5.H5Eget_msg(-1, null);
     }
 
     @Test
-    public void testH5Ecreate_stack() {
+    public void testH5Ecreate_stack()
+    {
         try {
             long stack_id = H5.H5Ecreate_stack();
             assertTrue("H5.H5Ecreate_stack", stack_id > 0);
@@ -286,14 +302,16 @@ public class TestH5Edefault {
     }
 
     @Test(expected = IllegalArgumentException.class)
-    public void testH5Eset_current_stack_invalid_stkid() throws Throwable {
+    public void testH5Eset_current_stack_invalid_stkid() throws Throwable
+    {
         H5.H5Eset_current_stack(-1);
     }
 
     @Test
-    public void testH5Eset_current_stack() {
-        long num_msg = -1;
-        long stack_id = -1;
+    public void testH5Eset_current_stack()
+    {
+        long num_msg       = -1;
+        long stack_id      = -1;
         long saved_num_msg = -1;
 
         // Generate errors on the default stack
@@ -301,7 +319,7 @@ public class TestH5Edefault {
             H5.H5Fopen("test", HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
         }
         catch (Throwable err) {
-            //err.printStackTrace(); //This will clear the error stack
+            // err.printStackTrace(); //This will clear the error stack
         }
 
         // Verify we have a nonzero number of messages and save it
@@ -324,7 +342,8 @@ public class TestH5Edefault {
             fail("H5.H5Eset_current_stack: " + err);
         }
         assertFalse("H5.H5Eset_current_stack: get_current_stack - " + stack_id, stack_id < 0);
-        assertFalse("H5.H5Eset_current_stack: get_current_stack - " + stack_id, stack_id == HDF5Constants.H5E_DEFAULT);
+        assertFalse("H5.H5Eset_current_stack: get_current_stack - " + stack_id,
+                    stack_id == HDF5Constants.H5E_DEFAULT);
 
         // Verify the copy has the same number of messages as the original stack
         try {
@@ -341,7 +360,7 @@ public class TestH5Edefault {
             H5.H5Fopen("test", HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
         }
         catch (Throwable err) {
-            //err.printStackTrace(); //This will clear the error stack
+            // err.printStackTrace(); //This will clear the error stack
         }
 
         // Verify we have the same number of messages as before
@@ -388,13 +407,15 @@ public class TestH5Edefault {
     }
 
     @Test(expected = IllegalArgumentException.class)
-    public void testH5Epop_invalid_stkid() throws Throwable {
+    public void testH5Epop_invalid_stkid() throws Throwable
+    {
         H5.H5Epop(-1, 0);
     }
 
     @Test
-    public void testH5Epop() throws Throwable {
-        long num_msg = -1;
+    public void testH5Epop() throws Throwable
+    {
+        long num_msg       = -1;
         long saved_num_msg = -1;
         try {
             H5.H5Fopen("test", HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
@@ -422,28 +443,33 @@ public class TestH5Edefault {
     }
 
     @Test(expected = IllegalArgumentException.class)
-    public void testH5Epush_invalid_stkid() throws Throwable {
+    public void testH5Epush_invalid_stkid() throws Throwable
+    {
         H5.H5Epush(-1, "Invalid", "Invalid", 0, -1, -1, -1, "Invalid message");
     }
 
     @Test(expected = NullPointerException.class)
-    public void testH5Epush_null_name() throws Throwable {
-        H5.H5Epush(HDF5Constants.H5E_DEFAULT, null, "Invalid", 0, HDF5Constants.H5E_DEFAULT, HDF5Constants.H5E_DEFAULT, HDF5Constants.H5E_DEFAULT, "Invalid message");
+    public void testH5Epush_null_name() throws Throwable
+    {
+        H5.H5Epush(HDF5Constants.H5E_DEFAULT, null, "Invalid", 0, HDF5Constants.H5E_DEFAULT,
+                   HDF5Constants.H5E_DEFAULT, HDF5Constants.H5E_DEFAULT, "Invalid message");
     }
 
     @Test(expected = IllegalArgumentException.class)
-    public void testH5EprintInt_invalid_classid() throws Throwable {
+    public void testH5EprintInt_invalid_classid() throws Throwable
+    {
         H5.H5Eprint2(-1, null);
     }
 
     @Ignore
-    public void testH5EprintInt() {
+    public void testH5EprintInt()
+    {
         /*
-        * If HDF5_VOL_CONNECTOR is set, this might not be the
-        * native connector and the error stack might be different.
-        * Only check for the specific error stack if the native
-        * connector is being used.
-        */
+         * If HDF5_VOL_CONNECTOR is set, this might not be the
+         * native connector and the error stack might be different.
+         * Only check for the specific error stack if the native
+         * connector is being used.
+         */
         String connector = System.getenv("HDF5_VOL_CONNECTOR");
         if (connector == null) {
             try {
@@ -462,7 +488,8 @@ public class TestH5Edefault {
     }
 
     @Test
-    public void testH5EclearInt() {
+    public void testH5EclearInt()
+    {
         try {
             H5.H5Eclear(HDF5Constants.H5E_DEFAULT);
         }
@@ -473,12 +500,14 @@ public class TestH5Edefault {
     }
 
     @Test(expected = IllegalArgumentException.class)
-    public void testH5Eclear2_invalid_stkid() throws Throwable {
+    public void testH5Eclear2_invalid_stkid() throws Throwable
+    {
         H5.H5Eclear2(-1);
     }
 
     @Test
-    public void testH5Eclear() {
+    public void testH5Eclear()
+    {
         try {
             H5.H5Eclear2(HDF5Constants.H5E_DEFAULT);
         }
@@ -489,7 +518,8 @@ public class TestH5Edefault {
     }
 
     @Test
-    public void testH5Eclear2_with_msg() {
+    public void testH5Eclear2_with_msg()
+    {
         long num_msg = -1;
         try {
             H5.H5Fopen("test", HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
@@ -516,12 +546,14 @@ public class TestH5Edefault {
     }
 
     @Test(expected = IllegalArgumentException.class)
-    public void testH5Eauto_is_v2_invalid_stkid() throws Throwable {
+    public void testH5Eauto_is_v2_invalid_stkid() throws Throwable
+    {
         H5.H5Eauto_is_v2(-1);
     }
 
     @Test
-    public void testH5Eauto_is_v2() {
+    public void testH5Eauto_is_v2()
+    {
         boolean is_v2 = false;
         try {
             is_v2 = H5.H5Eauto_is_v2(HDF5Constants.H5E_DEFAULT);
@@ -534,12 +566,14 @@ public class TestH5Edefault {
     }
 
     @Test(expected = IllegalArgumentException.class)
-    public void testH5Eget_num_invalid_stkid() throws Throwable {
+    public void testH5Eget_num_invalid_stkid() throws Throwable
+    {
         H5.H5Eget_num(-1);
     }
 
     @Test
-    public void testH5Eget_num() {
+    public void testH5Eget_num()
+    {
         long num_msg = -1;
         try {
             num_msg = H5.H5Eget_num(HDF5Constants.H5E_DEFAULT);
@@ -552,7 +586,8 @@ public class TestH5Edefault {
     }
 
     @Test
-    public void testH5Eget_num_with_msg() {
+    public void testH5Eget_num_with_msg()
+    {
         long num_msg = -1;
         try {
             H5.H5Fopen("test", HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
@@ -568,6 +603,4 @@ public class TestH5Edefault {
         }
         assertTrue("H5.H5Eget_num_with_msg #:" + num_msg, num_msg > 0);
     }
-
 }
-