| Commit message (Collapse) | Author | Age | Files | Lines |
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* Fixed -Wreserved-id-macro warnings from header include guards
* Removed all __int64 and LL suffix stuff now that C99 is minimum requirement
* Rename `H5FD_CTL__` to `H5FD_CTL_` to fix -Wreserved-id-macro warnings
Double underscore is reserved in C++ and this public header should be C++ compatible.
* Never define __STDC_FORMAT_MACROS anymore
Defining it causes a -Wreserved-id-macro.
Happily, according to the C++11 standard:
"The macros defined by <stdint> are provided unconditionally. In particular, the symbols __STDC_LIMIT_MACROS and __STDC_CONSTANT_MACROS (mentioned in C99 footnotes 219, 220, and 222) play no role in C++."
https://cplusplus.github.io/LWG/issue984
So looks like it's not necessary to define it with reasonably new toolchains.
* Fixed some -Wunused-macros warnings, removed dead code
* Fixed all -Wdouble-promotion warnings in C++ files
* Fixed remaining -Wsuggest-destructor-override warnings
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Synch update
* Branch sync changes
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* Flip inits to correct ifdef section
* rework ifdef to be simpler
* format issue
* Reformat ifdef inits
* remove static attribute
* format compliance
* Update names
* Revert because logic relies on float not being int
* Changes noticed from creating merge of #412
* Double underscore change
* Correct compiler version variable used
* Remove header guard underscores
* Whitespace cleanup
* Split format source and commit changes on repo push
* remove pre-split setting
* Change windows TS to use older VS.
* correct window os name
* HDFFV-11212 JNI export util and Javadoc
* Suggested review changes
* Another change found
* Committing clang-format changes
* HDFFV-11113 long double in tools
* HDFFV-11113 add note
* Disable long double tests for now
* HDFFV-11228 remove arbitrary CMake warning groups.
* Make each flag a string
* Some Javadoc warning fixes
* Updated javadoc fixes
* # WARNING: head commit changed in the meantime
HDFFV-11229 Fix long double usage in tools and java
Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.
* Committing clang-format changes
* HDFFV-11229 Add release note
* HDFFV-11229 windows testfile needed
* fix typo
* Remove non supported message text
* HDFFV-11229 - change ldouble test to check both native and general
* HDFFV-11229 add second file compare
* HDFFV-11229 fix reference file
* HDFFV-11229 autotools check two refs
* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output
* Committing clang-format changes
* Update release note
* Update attribute type of ref file
* Change source of ninja for macs
* try port instead of brew
* Recommended is to use brew.
* Undo non long double changes
* remove unneeded file
* Fix perl and doxygen CMake code
* Add "option" command for clang options
* Rework CMake add_custom to use the BYPRODUCTS argument
* Add stamp files to BYPRODUCTS
* Only one copy of file exists
* Fix custom cmmand depends targets
* Fix fortran custom command DEPENDS
* Add LD_LIBRARY_PATH to tests
* Add custom target for DEPENDS
* Add h5detect conditionaly to generated target DEPENDS
* Correct DEPENDS targets
* Parallel builds need the mpi compiler for pkgconfig scripts.
* install only if MPI build
* Fortran target depends
* Remove incorrect source attribute
* doxygen adjustments
* doxygen build updates
* Correct version
* Correct function version - function has been merged to 1.12
* Correct version string for map functions
* Cleanup warnings for tools debug builds
* TRILAB-227 - fix indexing for h5diff selections
* Correct location of pos to index function call
* TRILAB-227 Enable test
* Quote subset args
* Use MATCHES because of AppleClang
* if blocks needed for build modes
* Update list of DT platforms
* VS2019 correctly displays float values
* revert VS2019 change
* Issue #669 remove version from pkgcfg filename
* remove version from h5cc script
* Java reference functions updated
enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging
* Correct BYPRODUCTS argument
* Correct more genereated files BYPRODUCTS
* BYPRODUCTS must have unique locations
* Fix typo
* Fix fortran configure checks
* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic
* Add note about fortran configure change
* Adds a quick for for some egregious chunk_info badness (#722)
* Fixes issue with ccmake that prevents building Fortran (#723)
ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations
* Fix conflicts with merge
* Move MAX_PRECISION back to HDF5UseFortran.cmake
* Use STREQUAL to test macro argument
* Move C language test to ConfigureChecks from HDF5UseFortran
* MAX_PRECISION defines must be defined
* Organize flags and align autotools and cmake
* Fix comment in no-error-general warnings files.
* Flag cleanup and fix typos
* Add comment
* Correct VAR used to find configure time file
* Set the path correctly
* Update missing release note info.
* Update code owners
* Correct JIRA note
* add known problem.
* Use only core library for testing dynamic plugins.
* Committing clang-format changes
* Update main.yml
* Update HISTORY-1_13.txt
Missing release note added for changed location of CMake configuration files.
* Update HISTORY-1_13.txt
Fix typo
* Update main.yml
revert change
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
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* Committing clang-format changes
* Spelling of preceed was corrected to proceed, but should have been
corrected to precede.
* Correct spelling correction of 'preceed' incorrectly to 'proceed'. It should be 'precede'.
* Update version to 1.13.2-1 after 1.13.1 release.
Add Makefile.in to MANIFEST for addition of utils/tools and h5dwalk.
* Update VERS_RELEASE_EXCEPTIONS with new incompatible release version.
* Add HDF5 1.13.1 RELEASE.txt to HISTORY-1_13.txt contents to
HISTORY-1_13.txt.
Clean entries from RELEASE.txt.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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to MANIFEST (#1460)
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failure (#1458)
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* Add release note for #1438
* fix typos.
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Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
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(#1358)" (#1437)
This reverts commit 01092658a3095c31d7dc1ed1beebbd965095c244.
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* Add -showconfig to h5cc scripts to dump libhdf5.settings file
* Added note
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When resizing a pinned/protected cache entry, the metadata
cache code previously would wait until after resizing the
entry to attempt to log the newly-dirtied entry. This would
cause H5C_resize_entry to mark the entry as dirty and make
H5AC_resize_entry think that it doesn't need to add the
newly-dirtied entry to the dirty entries skiplist.
Thus, a subsequent H5AC__log_moved_entry would think it
needs to allocate a new entry for insertion into the dirty
entry skip list, since the entry doesn't exist on that list.
This causes an assertion failure, as the code to allocate a
new entry assumes that the entry is not dirty.
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* Fix several places where rank 0 can skip past collective MPI operations on failure
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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(#1355)
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Convert SWMR shell scripts to Windows powershell.
* Use $LastExitCode instead of $? in script
* Prevent execution in a different window
* Github #969 Use stdout instead of file for configure check (#1089)
* 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
* Don't allow H5Pset(get)_all_coll_metadata_ops for DXPLs (#1201)
* Fixes const warnings in H5ES package (#1211)
* Quiets a 'set but not used' warning in h5diff_array.c (#1210)
* Convert vds swmr test script to powershell
* Enable vdsswmr powershell test
* Add configure vdsswmr statement
* Correct powershell script vars
* Convert SWMR shell scripts to Windows powershell.
* Use $LastExitCode instead of $? in script
* Prevent execution in a different window
* Github #969 Use stdout instead of file for configure check (#1089)
* 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
* Convert vds swmr test script to powershell
* Enable vdsswmr powershell test
* Add configure vdsswmr statement
* Correct powershell script vars
* Cleanup review issues
* Fix variable assignment
* Change the wait function to pass in the path
* Disable actual test execution until programs fixed
* Adjust copyright text
* Fix spelling
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
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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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* Fixes an assert in H5Pget_filter_by_id1/2 w/ out-of-range IDs
Filter IDs < 0 or > H5Z_FILTER_MAX could trip an assert in the
library due to missing ID range checks in H5Pget_filter_by_id1/2.
The library now returns a normal error code when filter IDs are
out of range. Fixes HDFFV-11286.
* Committing clang-format changes
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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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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* H5repack tests should fail if a corrupted file causes h5repack to
segfault/core dump.
* Add release note for HDFV-10590, CVE-2018-17432.
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* Add release note for HDFFV-11150 fix.
* Add note about gif tool CVEs.
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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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No testing yet.
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* Update compact dataset I/O routines to handle driver-level memory copy
* Combine compact I/O read/write struct into single I/O struct
Rename CTL memory copy flag and H5Fquery routine to get file driver
structure
* Add RELEASE.txt entry for new "ctl" memory copy operation
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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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* Added "ctl" callback to the VFD interface, and the associated
H5FDctl() and H5FD_ctl() calls.
Modified the MPIO VFD accordingly -- specifically:
Added ctl() call with op-code support to expose rank, size,
and communicator.
Modified H5FD_mpi_get_rank(), H5FD_mpi_get_size(),
and H5FD_mpi_get_comm() to use the new ctl() callback. In passing
removed the const qualifier from the file parameter of these
functions, as the file parameter of the ctl callback is not
const.
Deleted the old H5FD__mpio_mpi_rank(), H5FD__mpio_mpi_size(), and
H5FD__mpio_communicator() calls from the MPIO VFD.
Deleted H5FD_class_mpi_t from H5FDprivate.h, and modified the
MPIO VFD accordingly. Note that all VFDs now use H5FD_class_t,
with no special class for VFDs that that support MPI.
Some minor touch ups to the Neil's selection I/O mods in passing.
Tested serial and parallel, debug and production on charis and
jelly.
* Reserve a range of VFD "ctl" opcodes for library and experimental usage
* Add "ctl" callbacks to passthrough VFDs
* Add RELEASE.txt entry for "ctl" callback
* Use H5FDopen with H5F_ACC_RDWR flag instead of H5F_ACC_TRUNC in vfd test
* Remove handling of passthrough "ctl" flag from multi VFD
* Move logic for testing H5FD_CTL__TEST_OPCODE into a testing VFD
Revise description of "ctl" callback in RELEASE.txt
Remove unused H5FD_CTL__NUM_OPCODES definition
Fix some warnings in multi VFD
Co-authored-by: mainzer <mainzer#hdfgroup.org>
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* HDFFV-11266 - add option to build HL tools
* Correct if syntax
* Correct name of conditional
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* H5Ztrans: (feature) Improved H5Z_xform_noop() and H5Z_xform_create() function
- Made a small improvement for H5Z_xform_noop() function. Now,
the function will also return TRUE if the data transform function
expression = "x". For this case, the HDF5 library behaves in a
similar fashion as the case when no data transform function has been
specified.
- Improved the inline documentation of the function
H5Z_xform_create() such it is more inline with the rest of the
code.
* Committing clang-format changes
* H5Ztrans: (feature) Added 3 tests for improved H5Z_xform_noop() function
- Added serial test with data transform expression = "x" to
verify the improved H5Z_xform_noop() function behaves as expected.
- Added 2 parallel tests with data transform expression = "x"
in combination with a filter. Before, these tests will fail but
with the improved H5Z_xform_noop() function they work and result
in the expected behavior.
- Small bug fix for one of parallel filter tests.
* Committing clang-format changes
* H5Ztrans: (feature) Added release note about detection of the
simple data transform function "x".
- Added a brief explanation about the implemented improvement
of the detection of the simple data transform function "x"
to the RELEASE.txt file.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* add ULL attr set/get signatures to LT public API
* add LT implementation of ULL set/get attribute
* fix copy-paste typo in test comment
* add ULL test data
* define ullong attr name global variable
* add LT tests for ULL attr set/get
* Committing clang-format changes
* correct type passed to lt get attr test for ULL
* update RELEASE.txt with added ULL set/get functionality
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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* Correction of pkg-config compile script.
* Reword note.
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Change doxygen generated file location
Clang format override for flags
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* H5Fget_name_f fixed to handle correctly trailing whitespaces and newly allocated buffers.
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
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