| Commit message (Collapse) | Author | Age | Files | Lines |
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Sync with develop
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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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* Change ENV to CMake var
* Fix typo deletion
* Fix typo
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to MANIFEST (#1460)
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* Add release note for #1438
* fix typos.
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* Updated plugins project required adjustments
* Updated plugins need to distinguish external libs
* Fix missed rename
* Use same name for windows as linux - avoid name clash
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* Add -showconfig to h5cc scripts to dump libhdf5.settings file
* Added note
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* Replaced several uses of sprintf with safer snprintf
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Fix sanitizer flag form on windows
* Add search paths to windows code-coverage
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* H5Lexists docs: Removed reference to 1.8.16 since the change is the 1.8.x releases, HDFFV-11289
* H5Oget_info_by_name, name can be any object, not just a group
* Converted README.txt to README.md and updated files referring to README.txt to README.md.
* removed references to README.txt
* updated MANIFEST
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* fixed missed closing of a dataset
* fixed missed closing of a dataset
* fixed typo in error return
* Committing clang-format changes
* minor edits
* code format
* Committing clang-format changes
* code format
* minor edit
* switched from using MPI_count, to actual bytes written for H5FD_mpio_debug rw debugging
* Committing clang-format changes
* changed size_i in printf to reflect the I/O.
* Committing clang-format changes
* Fixed seg fault with xlf on BE with -qintsize=8
* fixed error function string
* spelling corrections via codespell, added new spell check github actions
* Committing clang-format changes
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* misc
* Committing clang-format changes
* misc
* misc
* misc
* misc
* misc
* misc
* Committing clang-format changes
* misc
* work around for https://github.com/codespell-project/codespell/issues/2137
* misc
* added missing file
* misc
* misc.
* misc
* switch to using Codespell with GitHub Actions
* misc.
* misc.
* fixed more sp errors
* Fix new typos found by codespell.
* fixed proceed with precede
* fixed variable in fortran test
* fixed minnum
* updated spelling list
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
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(libMFU) … (#1177)
Adds tool h5dwalk and configure options to enable building it.
Co-authored-by: Richard Warren <Richard.Warren@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Richard.Warren <richard.warren@jelly.ad.hdfgroup.org>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
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* Fix order of fortran define
* fix typo
* Fix REGEX and newlines
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* Use stdout instead of file for configure check
* Make change requested by #1157
* Change fortran to use stderr for configure
* Correct typo
* remove obsolete file check
* Fortran statement fix
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gnu-warnings (unrecognized command line option for gcc 4.85/4.93.
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pointer or from pointer to integer (-Werror=int-conversion). Also,
make it an error if the library explicitly converts to pointer from an
integer of a different size (-Werror=int-to-pointer-cast).
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`-Werror=cast-function-type`. Again.
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* Enable usage of new-style references with dimension scale APIs
* Add API to check if an object ID represents a native connector object
* Modified code to use new function H5DSwith_new_ref to determine if new references should be used with
Dimension Scales. The new function return TRUE if non-native connector is used or if H5_DIMENSION_SCALES_WITH_NEW_REF
varible is define at configure time (--enable-dimension-scales-with-new-ref).
Tested on jelly.
ToDo: generate testing file on BE system and enable the test; add flag to CMake; test netCDF-4 with the new references.
* Adding new test files generated on BE system (hedgehog) created by 32 and 64-bit library.
test_ds chokes on test_ds_le_new_ref.h5 on BE system; test passes for test_ds_be_new_ref-32bit.h5
for the 32-bit library and fails for the 64-bit library, and vice versa. I am checking the files for further
investigation; but current implementation of the new references is not portable between LE and BE systems,
and 32 and 64-bit systems.
* Minor fixes for testing issues
* Update test_ds.c
Enabled broken test; tests pass now.
* Update RELEASE.txt
Documented new option to use new references with the HDF5 dimension scales APIs (H5DS*).
* Update MANIFEST for new 32-bit new-style references test file for H5DS APIs
* Update 'dimension scales w/ new-style refs' feature based on review
Co-authored-by: Elena <epourmal@hdfgroup.org>
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* Split dir create into separate macro
* Correct VFD settings
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* Move test utilities to utils/test folder
* Fix makefile assignment
* Add new dir
* add new folder
* Correct copied makefile
* Fix dir typo
* Add missing include dir
* Remove unnecessary lib link
* Correct dependent dirs
* Fix conditional checks
* Disable test if not built
* fix path to executable
* Use fixture for swmr_vfd check
* Add release note
* Correct shell tests and c++ flag warning
* Update autotools c++ warning
* Fix typo
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flags files (#1033)
* Avoid maintenance headaches: delete the `noerror-` variants of the
compiler flags files, since they essentially duplicate the `error-`
files modulo the replacement of `-Werror=` with `-W` and any changes in
comments. (I verified the duplication with a script.)
For autoconf, reinstate the use of the `demote_errors` shell function to
derive the `noerror-` content from the `error-` content. `demote_errors`
replaces `-Werror=` with `-W` when `WARNINGS_AS_ERRORS` is `no`.
Slightly reorder `configure.ac` so that the setting of
`WARNINGS_AS_ERRORS` takes effect before the `error-` files are sourced.
* Take a stab at updating the CMake files to match the changes I made to
the autoconf files to remove `noerror-` files. I'm not much of a CMake
user so these changes are quite rough.
Looks like the duplication can be reduced with the introduction of a new
macro.
* Delete `noerror-` files from the MANIFEST.
* Reduce duplication in the CMake files: perform the
HDF5_ENABLE_WARNINGS_AS_ERRORS test once in the ADD_H5_FLAGS macro.
* Add a release note.
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* Implement support for loading of Virtual File Drivers as plugins
Fix plugin caching for VOL connector and VFD plugins
Fix plugin iteration to skip paths that can't be opened
* Enable dynamic loading of VFDs with HDF5_DRIVER environment variable
* Temporarily disable error reporting during H5F_open double file open
* Default to using HDstat in h5_get_file_size for unknown VFDs
* Use macros for some environment variables that HDF5 interprets
* Update "null" and "ctl testing" VFDs
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* Update Platforms Tested in RELEASE.txt.
Remove Tested Configuration Features Summary for updated replacement.
* Set version to 1.13.0-6 for rc6 snapshot.
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* Corrected path searched by CMake find_package command
* Correct path for depend libs
* Adjust examples script for install path
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* Upgrade libaec to 1.0.6
* correct include file name
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* HDFFV-11266 - add option to build HL tools
* Correct if syntax
* Correct name of conditional
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* Correction of pkg-config compile script.
* Reword note.
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