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>

3 files changed, 13 insertions, 6 deletions

diff --git a/.github/workflows/clang-format-check.yml b/.github/workflows/clang-format-check.yml
index 4f696e7..0343f4b 100644
--- a/.github/workflows/clang-format-check.yml
+++ b/.github/workflows/clang-format-check.yml
@@ -8,11 +8,11 @@ jobs:
     if: "!contains(github.event.head_commit.message, 'skip-ci')"
     steps:
     - uses: actions/checkout@v2
-    - name: Run clang-format style check for C programs.
+    - name: Run clang-format style check for C and java programs.
       uses: DoozyX/clang-format-lint-action@v0.11
       with:
         source: '.'
-        extensions: 'c,h,cpp,hpp'
+        extensions: 'c,h,cpp,hpp,java'
         clangFormatVersion: 10
         style: file
         exclude: './config ./hl/src/H5LTanalyze.c ./hl/src/H5LTparse.c ./hl/src/H5LTparse.h ./src/H5Epubgen.h ./src/H5Einit.h ./src/H5Eterm.h ./src/H5Edefin.h ./src/H5version.h ./src/H5overflow.h'
diff --git a/.github/workflows/clang-format-fix.yml b/.github/workflows/clang-format-fix.yml
index 082d617..abdd069 100644
--- a/.github/workflows/clang-format-fix.yml
+++ b/.github/workflows/clang-format-fix.yml
@@ -9,11 +9,11 @@ jobs:
     if: "!contains(github.event.head_commit.message, 'skip-ci')"
     steps:
     - uses: actions/checkout@v2
-    - name: Run clang-format style check for C programs.
+    - name: Run clang-format style check for C and Java programs.
       uses: DoozyX/clang-format-lint-action@v0.11
       with:
         source: '.'
-        extensions: 'c,h,cpp,hpp'
+        extensions: 'c,h,cpp,hpp,java'
         clangFormatVersion: 10
         inplace: True
         style: file
diff --git a/.github/workflows/pr-check.yml b/.github/workflows/pr-check.yml
index 65bf42b..5dd923f 100644
--- a/.github/workflows/pr-check.yml
+++ b/.github/workflows/pr-check.yml
@@ -1,10 +1,17 @@
-name: hdf5 dev CI
+name: PR hdf5 dev CI
 
 # Controls when the action will run. Triggers the workflow on push or pull request
 on:
   pull_request:
     branches: [ develop, hdf5_1_12, hdf5_1_10, hdf5_1_8 ]
-
+    paths-ignore:
+    - '.github/**'
+    - 'doc/**'
+    - 'release_docs/**'
+    - 'ACKNOWLEDGEMENTS'
+    - 'COPYING**'
+    - '**.md'
+ 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   # This workflow contains a single job called "build"