| Commit message (Collapse) | Author | Age | Files | Lines |
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* 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>
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* Modify temporary rpath for testing in java example scripts.
* Update URL in source file Copyright headers for web copy of COPYING
file - files not in src or test.
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Description:
Applied the typo fixes from user's report.
The previous pull request couldn't be merged because it was too old,
and it was too complicated for me to resolve conflicts.
Platform tested:
Linux/64 (jelly) - very minor
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hdf5_1_10
* commit '54957d37f5aa73912763dbb6e308555e863c43f4':
Commit copyright header change for src/H5PLpkg.c which was added after running script to make changes.
Add new files in release_docs to MANIFEST. Cimmit changes to Makefile.in(s) and H5PL.c that resulted from running autogen.sh.
Merge pull request #407 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10_1 to hdf5_1_10_1
Change copyright headers to replace url referring to file to be removed and replace it with new url for COPYING file.
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so that script failures leave the library in a non-compilable state,
making it harder to ignore errors.
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- autogen.sh now exits on unknown arguments
Tested on: 64-bit Ubuntu 15.10 w/ gcc 5.2.1
autotools serial
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This was giving a lot of users headaches and the parser code rarely
changes. There is now a new script (bin/genparser) which can be
run as needed.
Tested on: Ubuntu 15.10 (x86_64 Linux 4.2.0)
gcc 5.2.1, flex 2.5.39, bison 3.0.2
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hard-coded version checks.
Tested on: jam
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H5LTparse.c
- this is needed when running autogen on a couple of HPC machines.
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- Removed the long options, which are not supported under
the getopts builtin.
- Correctly labeled the autogen.sh script as requiring bash
(via the #!). We may need to remove the bash constructs
before the 1.10 release and revert to sh.
- The help output is now correct.
Tested on: local linux
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flex/bison.
Tested on: local linux
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instead of symlinks.
Tested on: local linux
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The files in the m4 directory were not getting picked up on some platforms.
Tested on: jam
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Tested on: jam (too minor for h5committest)
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Removes .pl extension from Perl scripts. This may be returned in the future,
but it's best to keep the script names unchanged while we merge with the
trunk.
Tested on: h5committest
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This makes things easier on Windows, where we will have to run
Perl scripts as a part of CMake.
Tested on: jam
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from the trunk.
Fixes: HDFFV-9149
Tested on: jam
- examined gcc 4.9.2 output for warnings
- ran 'make check' in hl directory
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and then fall back to libtoolize if not found.
Tested on OS X 10.10.2 (Yosemite) with Xcode 6.1.1 and autotools
installed via Brew
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Fixes: HDFFV-9098
Tested on: 64-bit linux VM (autogen only)
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that causes a circular dependency issue.
Tested on: 64-bit linux VM (autogen only - just a comment change)
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Remove generated header file from repository, and add section to
autogen.sh that generates it.
Tested on:
Mac OSX/64 10.10.2 (amazon)
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--add-missing;
it's not a replacement.
Part of HDFFV-9114
Tested on jam with the -p option
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Part of HDFFV-9114
Tested on: Cygwin
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when available. Also added the --copy option to to libtoolize
so files are copied and not symlinked.
Part of HDFFV-9114
Tested on jam.
- autogen.sh -p
- configure (out-of-source)
- Modified configure.ac
- Re-run autogen.sh -p
- Re-run configure
- make
Without the fix, make fails when it notes out-of-date autotools
files and re-runs the tools, picking up jam's elderly versions.
With the fix, make succeeds.
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Tested on: jam w/ Fortran and C++
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installing the autotools via a package manager like Homebrew since
they are not installed with XCode.
Part of: HDFFV-9114
Tested on: OS-X 10.10.2 (Yosemite) with XCode 6.1.1
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(incomplete)
bin/genltanalyze script, which has been deleted. Also removed the
generated hl/src/H5LTparse.c/h and H5LTanalyze.c files.
Part of: HDFFV-9120
Tested on: Local Ubuntu VM
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the -s option from autogen.sh. Removed several generated H5E
files from version control as well as H5version.h since these
will always be regenerated.
Part of: HDFFV-9120
Tested on: Local Ubuntu VM
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not found. Allows reconfiguration on OS-X.
Part of: HDFFV-9120
Untested since we have no suitable OS-X machines
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autotools
re-builds, which would fail due to incorrect autotools versions.
Part of: HDFFV-9120
Tested on: jam
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- Modified autogen.sh to run libtoolize.
NOTE: OS-X often uses glibtoolize. This will be fixed soon.
- Addational helpful output added to autogen.sh.
Part of HDFFV-9120
Tested on: 64-bit Linux VM
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Part of HDFFV-9114
Tested on: jam
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Note that bin/reconfigure still exists. It will be removed at a later
date.
Part of HDFFV-9114
Tested on: jam
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